Scientific software installed on BIOMIX computational cluster at the Delaware Biotechnology Institute, University of Delaware
BIOMIX questions/comments should be addressed to Karol Miaskiewicz at miaskiew@udel.edu
If information about PATH variable is not provided in the program description below, it implies that the program resides in default user PATH, as configured on Biomix. In other words, you do not need to modify your PATH to use the program - typing programs name is enough to launch it (plus additional arguments that the program may require).
AMOS version 3.1.0
http://amos.sourceforge.net/wiki/index.php/AMOS
AMOS is a modular, open-source whole genome assembler. It is installed at /usr/local/amos.
To use:
PATH:/usr/local/amos/bin
AmpliconNoise version 1.29
http://code.google.com/p/ampliconnoise/
AmpliconNoise is a collection of programs for the removal of noise from 454
sequenced PCR amplicons. It is installed at /usr/local/AmpliconNoise.
To use:
source /etc/dbi/ampnoise_env
ART version MountRainier-2016-06-05
https://www.niehs.nih.gov/research/resources/software/biostatistics/art/
ART is a set of simulation tools to generate synthetic next-generation sequencing reads.
It supports simulation of single-end, paired-end/mate-pair reads of three next-generation
sequencing platforms: Illumina's Solexa, Roche's 454 and Applied Biosystems' SOLiD.
ART is installed at /usr/local/ART. To use:
PATH=$PATH:/usr/local/ART
ASCIIGenome version 1.17
https://github.com/dariober/ASCIIGenome
ASCIIGenome is a command-line genome browser running from terminal window and solely based
on ASCII characters. Since ASCIIGenome does not require a graphical interface it is
particularly useful for quickly visualizing genomic data on remote servers.
Augustus version 3.5.0
http://bioinf.uni-greifswald.de/augustus/
Augustus is a program that predicts genes in eukaryotic genomic sequences. It
is installed at /usr/local/Augustus.
Bamtools version 2.5.1
https://github.com/pezmaster31/bamtools/wiki/
Bamtools is a command-line toolkit to manipulate BAM files.
Barrnap version 0.9
https://github.com/tseemann/barrnap/
BAsic Rapid Ribosomal RNA Predictor
(Barrnap) predicts the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), metazoan mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).
It is installed at /usr/local/barrnap. To use:
PATH=$PATH:/usr/local/barrnap/bin
Batmis version 3.00
https://code.google.com/archive/p/batmis/
Batmis is a short read aligner allowing up to 10 mismatches.
BBTools version 39.01
https://jgi.doe.gov/data-and-tools/bbtools/
BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of
DNA and RNA sequence data. BBTools can handle common sequencing file formats such as fastq,
fasta, sam, scarf, fasta+qual, compressed or raw, with autodetection of quality encoding and
interleaving.
The BBTools suite includes programs such as:
• bbduk – filters or trims reads for adapters and contaminants using k-mers
• bbmap – short-read aligner for DNA and RNA-seq data
• bbmerge – merges overlapping or nonoverlapping pairs into a single reads
• reformat – converts sequence files between different formats such as fastq and fasta
BBTools are installed at /usr/local/bbmap. To use, append the PATH variable:
PATH=$PATH:/usr/local/bbmap
Bcftools version 1.17
https://github.com/samtools/bcftools
BCFtools is a set of utilities that manipulate genomic variant calls in the
Variant Call Format (VCF) and its binary counterpart (BCF).
BEDtools version 2.30.0
https://github.com/arq5x/bedtools2/
Bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. For instance, it allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF.
Biopieces version 2.0.12
http://maasha.github.io/biopieces/
The Biopieces are a collection of bioinformatics tools that can be pieced together in a very easy
and flexible manner to perform both simple and complex tasks. The Biopieces work on a data stream in
such a way that the data stream can be passed through several different Biopieces, each performing one
specific task: modifying or adding records to the data stream, creating plots, or uploading data to
databases and web services. The Biopieces are executed in a command line environment where the data
stream is initialized by specific Biopieces which read data from files, databases, or web services,
and output records to the data stream that is passed to downstream Biopieces until the data stream
is terminated at the end of the analysis.
Biopieces is installed at /usr/local/biopieces. Add the following lines to
your .bashrc file when working with Biopieces:
export BP_DIR="/usr/local/biopieces"
export BP_DATA="$HOME/BP_DATA"
export BP_TMP="/scratch"
export BP_LOG="$HOME/BP_LOG"
if [ -f "$BP_DIR/config/bashrc" ]; then
source "$BP_DIR/config/bashrc"
fi
You must create the directories named BP_DATA and BP_LOG under your home directory.
Note, that biopieces depend on a number of external applications. These applications must be
included in your PATH for biopieces to work correctly.
BLAST version 2.2.22
http://blast.ncbi.nlm.nih.gov/
Blast is a sequence alignment tool. This old version is required by some
other software packages. It is installed at /usr/local/blast-2.2.22. To use:
export PATH=/usr/local/blast-2.2.22/bin:$PATH
(For the latest version of BLAST - see entry for NCBI Blast+ below.)
BLAST+ version 2.15.0
http://blast.ncbi.nlm.nih.gov/
Blast is a sequence alignment tool. This is the latest version as of Jan 2024.
There appears to be a bug related to taxonomy filtering functions such as -taxids and -taxidlist.
To resolve this issue, please execute the following command in your blast job directory:
ln -s /usr/local/blastdb_v5/taxonomy4blast.sqlite3 .
BLAST databases
All available BLAST databases are located at:
/usr/local/blast_db
They were last updated in January 2019.
Version 5 databases, that can be efficiently utilized by latest NCBI Blast+ software, are located at:
/usr/local/blastdb_v5
They were last updated in January 2024.
BLAT version 37x1
http://genome.ucsc.edu/FAQ/FAQblat.html
Blat is a sequence alignment tool.
BlobTools version 1.1.1
https://blobtools.readme.io/docs
Command-line tool for visualisation, quality control, and taxonomic paritioning of genome datasets.
It is installed in /usr/local/blobtools. To use:
PATH=$PATH:/usr/local/blobtools
Bowtie2 version 2.5.1
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Bowtie2 is a new version of Bowtie - an ultrafast short read aligner.
It is installed at /usr/local/bowtie2. To use:
PATH=${PATH}:/usr/local/bowtie2
BreakDancer version 1.1.2
http://breakdancer.sourceforge.net/
BreakDancer provides genome-wide detection of structural variants from next generation paired-end sequencing reads.
It is installed at /usr/local/breakdancer. There are two components.
One is C++ program with compiled binary at /usr/local/breakdancer/bin/breakdancer.
The other one is a Perl script at /usr/local/breakdancer/perl/bam2cfg.pl.
Burrows-Wheeler Aligner (BWA) version 0.7.17
http://bio-bwa.sourceforge.net/
BWA aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.
It is installed at /usr/local/bwa. Main executable "bwa" is present in /usr/local/bin and does not require
adjusting PATH to start. However, if you want to use additional scripts and programs available as bwakit, add the
following location to your PATH variable:
PATH=$PATH:/usr/local/bwa/bwakit
Busco version 5.4.4
https://busco.ezlab.org/
The BUSCO tool suite can assess the completeness of genomes, gene sets, and transcriptomes, using their gene content
as a complementary method to common technical metrics.
You have to create Busco configuration file to match your environment.
The ``BUSCO_CONFIG_FILE`` environment variable defines the path (including the filename) to that ``config.ini`` file:
export BUSCO_CONFIG_FILE="/path/to/myconfig.ini"
You can copy /usr/local/busco/config/config.ini file and use it as a template for your configuration.
Bustools version 0.42
https://github.com/BUStools/bustools
Bustools is a program for manipulating BUS files for single cell RNA-Seq datasets. It can be used to error correct barcodes,
collapse UMIs, produce gene count or transcript compatibility count matrices, and it can be useful for many other tasks.
Canu version 2.2
https://github.com/marbl/canu
Canu is a fork, and the replacement, of the Celera Assembler (Celera's
development has been discontinued). It is designed for high-noise
single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION).
It is installed at /usr/local/canu. To use:
PATH=$PATH:/usr/local/canu/bin
Cdbfasta version 0.99
http://cdbfasta.sourceforge.net/
Cdbfasta is a fasta file indexing and retrival tool.
CD-HIT version 4.8.1
http://cd-hit.org/
CD-HIT is used for clustering and comparing protein or nucleotide sequences.
It is installed at /usr/local/cdhit. To use:
export PATH=$PATH:/usr/local/cdhit
CheckM version 1.2.2
https://github.com/Ecogenomics/CheckM/wiki
CheckM provides a set of tools for assessing the quality of genomes.
CheckM must be installed locally because of its required write permissions to configuration directory.
Install as follows:
pip install --user checkm-genome
PATH=~/.local/bin:$PATH
cp -r /usr/local/CheckmDB ~/CheckmDB
checkm data setRoot ~/CheckmDB
Chimera Slayer
http://microbiomeutil.sourceforge.net/
ChimeraSlayer is a chimeric sequence detection utility, compatible with
near-full length Sanger sequences and shorter 454-FLX sequences (~500 bp).
It is installed with other Microbiome Analysis Utilities tools from the
Broad Institute at /usr/local/microbiomeutil. To use:
export PATH=$PATH:/usr/local/microbiomeutil/ChimeraSlayer
Circlator version 1.5.5
https://sanger-pathogens.github.io/circlator/
Circlator is a tool to circularize genome assemblies. To use, you must have required software
dependencies in your PATH. If your PATH is the default, as provided by the system, the following
will work for circlator:
PATH=$PATH:/usr/local/MUMmer:/usr/local/canu/bin:/usr/local/SPAdes/bin
Clearcut version 1.0.9
https://github.com/ibest/clearcut/
Clearcut is an implementation of relaxed neighbor joining algoritm (RNJ) for
distance-based phylogenetic tree contruction.
Clustal Omega version 1.2.4
http://www.clustal.org/omega/
Clustal Omega is the latest tool in the Clustal family tools for multiple
sequence alignment.
CompareM version 0.1.2
https://github.com/dparks1134/CompareM
CompareM is a tool to perform large-scale comparative genomic analyses.
CONCOCT version 1.1.0
https://github.com/BinPro/CONCOCT
CONCOCT performs unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data
in multiple samples and linkage data from paired end reads.
CoverM version 0.6.1
https://github.com/wwood/CoverM
CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator
focused on metagenomics applications.
Cufflinks version 2.2.1
https://github.com/cole-trapnell-lab/cufflinks/
Cufflinks assembles transcripts, estimates their abundances, and tests for
differential expression and regulation in RNA-Seq samples.
Cutadapt version 4.4
https://cutadapt.readthedocs.org/
Cutadapt is a python tool to remove adapter sequences from high-throughput
sequencing data.
DAS_Tool version 1.1.6
https://github.com/cmks/DAS_Tool
DAS Tool is an automated method to integrate the results of a flexible number of binning algorithms to
calculate an optimized, non-redundant set of bins from a single assembly.
It is installed at /usr/local/DAS_Tool. To use:
PATH=$PATH:/usr/local/DAS_Tool
Diamond version 2.1.6.160
http://www.diamondsearch.org
DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance
analysis of big sequence data.
Dorado version 0.5.3
https://github.com/nanoporetech/dorado
Dorado is basecaller for Oxford Nanopore reads.
Dorado executes on Nvidia GPUs. You must use it on Biomix GPU-equipped nodes -
https://bioit.dbi.udel.edu/BIOMIX/SLURM-intro.html#GPU.
ea-utils version 1.04.807
https://expressionanalysis.github.io/ea-utils/
Command-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. Primarily written to support an Illumina based pipeline - but should work with any FASTQs.
EMBOSS version 6.6.0
http://emboss.sourceforge.net/
EMBOSS is the European Molecular Biology Open Software Suite
specially developed for the needs of the molecular biology user community.
Entrez Direct (EDirect)
https://www.ncbi.nlm.nih.gov/books/NBK179288/
Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected databases (publication, sequence,
structure, gene, variation, expression, etc.) from a UNIX command line. It is installed at /usr/local/edirect.
To use:
PATH=$PATH:/usr/local/edirect
Exonerate version 2.2
http://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate
Exonerate is a tool for pairwise sequence comparison. It allows you to align
sequences using many alignment models. It is installed at /usr/local/exonerate.
To use:
export PATH=$PATH:/usr/local/exonerate/bin
faSomeRecords
https://github.com/santiagosnchez/faSomeRecords
faSomeRecords is a python script to extract FASTA records from multiFASTA file based
on a list of FASTA headers.
FAST version 1.7
https://github.com/tlawrence3/FAST
The FAST Analysis of Sequences Toolbox (FAST) is a set of Unix tools
(for example fasgrep, fascut, fashead and fastr) for sequence bioinformatics
modeled after the Unix textutils (such as grep, cut, head, tr, etc).
FASTA verions 36.3.8i
http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml
The FASTA program can be used to search protein or DNA sequence data bases
and to compare a protein sequence to a DNA sequence data base by translating
the DNA data base as it is searched.
FastANI version 1.33
https://github.com/ParBLiSS/FastANI
FastANI provides fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI).
ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes.
FastQC version 0.11.9
http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
A quality control tool for high throughput sequence data. It is installed at /usr/local/FastQC. To use:
PATH=$PATH:/usr/local/FastQC
FastTree version 2.1.11
http://www.microbesonline.org/fasttree/
FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.
FastTree is the name of a serial (single-thread) executable. FastTreeMP is the name of a parallel (multi-threaded) executable.
FASTX-Toolkit version 0.0.14
http://hannonlab.cshl.edu/fastx_toolkit/
The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
Filtlong version 0.2.1
https://github.com/rrwick/Filtlong
Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset.
Type filtlong to start the program.
FLASH version 1.2.11
http://ccb.jhu.edu/software/FLASH/
FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate
software tool to merge paired-end reads from next-generation sequencing
experiments.
FoldMason Release 4-dd3c235
https://github.com/steineggerlab/foldmason/
FoldMason is a software tool for constructing accurate multiple alignments from large sets of protein structures.
It is installed at /usr/local/foldmason. To use:
export PATH=/usr/local/foldmason/bin:$PATH
FreeBayes version 1.3.2
https://github.com/ekg/freebayes
FreeBayes is a variant detecting tool designed to find small polymorphisms, specifically SNPs
(single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms),
and complex events (composite insertion and substitution events).
FreeBayes exectuables - freebays and bamleftaligh - should be already in your PATH, as they are located
/usr/local/bin. However, if you want to use auxiliary scripts that come with FreeBayes, you must
modify your PATH as follows:
PATH=PATH:/usr/local/freebayes/scripts
FR-HIT version 0.7
https://github.com/Beifang/fr-hit
FR-HIT performs fragment recruitment - a process of aligning sequencing reads
to reference genomes. It is installed at /usr/local/fr-hit. To use:
PATH=$PATH:/usr/local/fr-hit
gam-ngs version 1.1b
https://github.com/vice87/gam-ngs
Genomic Assemblies Merger for NGS - gam-ngs - can merge two or more assemblies
in order to enhance contiguity and correctness of both. It is installed at
/usr/local/gam-ngs. To use:
PATH=$PATH:/usr/local/gam-ngs/bin
GATK version 4.3.0.0
http://www.broadinstitute.org/gatk/
Genome Analysis Toolkit - GATK - is a software package developed at the Broad
Institute that provides a wide variety of tools to analyse next-generation
sequencing data. It is install at /usr/local/GATK. Use the launch script
/usr/local/gatk/gatk to start the program.
Geneid version 1.4.4
http://genome.crg.es/software/geneid/
Geneid predicts genes in anonymous genomic sequences designed with a
hierarchical structure.
GeneMark-ETP
https://github.com/gatech-genemark/GeneMark-ETP
Gene finding in eukaryotic genomes supported by transcriptome sequencing and
protein homology. To use:
&nbsl PATH=$PATH:/usr/local/GeneMark-ETP/bin
GenomeTools version 1.5.9
http://genometools.org/
The GenomeTools genome analysis system is a collection of bioinformatics tools
combined into a single binary named gt.
GroopM version 0.3.4
http://ecogenomics.github.io/GroopM/
GroopM is a metagenomic binning tool.
GTDB-Tk version 2.1.0
https://github.com/Ecogenomics/GTDBTk
GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes
based on the Genome Database Taxonomy (GTDB).
Before running you must set up the variable pointing to GTDB-Tk database:
export GTDBTK_DATA_PATH=/usr/local/GTDB-DB/release207_v2
GTDB-Tk depends on other software packages. All of the required packages should already be in your PATH except for pplacer.
If your pipeline requires pplacer:
PATH=$PATH:/usr/local/pplacer/bin:/usr/local/pplacer/scripts
GUSHR
https://github.com/Gaius-Augustus/GUSHR
Assembly-free construction of UTRs from short read RNA-Seq data on the basis of coding
sequence annotation.
This tool has been adapted to the format needs of AUGUSTUS/BRAKER and employs GeMoMa
for generating UTRs from RNA-Seq coverage data.
HISAT2 version 2.2.1
https://ccb.jhu.edu/software/hisat2/
HISAT2 is an alignment program for mapping next-generation sequencing reads (both DNA and RNA)
to a population of human genomes (as well as to a single reference genome).
It is installed at /usr/local/hisat2. To use:
PATH=$PATH:/usr/local/hisat2
HMMER version 3.3
http://hmmer.org
HMMER is used for searching sequence databases for sequence homologs, and for
making sequence alignments.
HTSeq version 0.11.2
https://github.com/simon-anders/htseq
HTSeq is a Python library to facilitate processing and analysis of data
from high-throughput sequencing experiments.
IDBA version 1.1.1
http://i.cs.hku.hk/~alse/hkubrg/projects/idba/
IDBA suite contains IDBA, IDBA-UD, IDBA-Tran, and IDBA-Hybrid programs.
IDBA is the basic iterative de Bruijn graph assembler for second-generation
sequencing reads. IDBA-UD, an extension of IDBA, is designed to utilize
paired-end reads to assemble low-depth regions and use progressive depth on
contigs to reduce errors in high-depth regions. It is a generic purpose
assembler and epspacially good for single-cell and metagenomic sequencing
data. IDBA-Hybrid is another update version of IDBA-UD, which can make use
of a similar reference genome to improve assembly result. IDBA-Tran is an
iterative de Bruijn graph assembler for RNA-Seq data.
IDBA is installed at /usr/local/idba. To use:
export PATH=$PATH:/usr/local/idba/bin
ImageJ version 4.0.5
https://imagej.net/
ImageJ is an open source image processing program designed for scientific multidimensional images. Note that
this is so-called "Fiji" version that is installed on Biomix.
Simply type ImageJ to launch.
Infernal version 1.1.3
http://eddylab.org/infernal/
Infernal is used to search DNA sequence databases for RNA structure and
sequence similarities.
inStrain version 1.8.0
https://instrain.readthedocs.io/en/latest/
InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows
highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and
sensitive SNP detection with gene localization and synonymous non-synonymous identification.
Integrative Genomics Viewer (IGV) version 2.8.0
http://www.broadinstitute.org/igv/
The Integrative Genomics Viewer (IGV) is a high-performance visualization
tool for interactive exploration of large, integrated genomic datasets. It
supports a wide variety of data types, including array-based and
next-generation sequence data, and genomic annotations.
It is installed
at /usr/local/IGV. Start the program with:
/usr/local/IGV/igv.sh
Note that is also IGV web-application that runs in a web browser. Check IGV
web site for details, if interested.
Jellyfish version 2.3.0
http://www.genome.umd.edu/jellyfish.html
Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.
Khmer version 3.0.0
https://github.com/dib-lab/khmer
http://khmer.readthedocs.io/en/v2.0/
Khmer is a python toolkit for doing k-mer-based dataset analysis and transformations.
KMC version 3.2.4
http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=kmc&subpage=about
KMC - K-mer Counter - is a very fast and memory frugal k-mer counting program. kmc,
kmc_tools, and kmc_dump programs are all installed in /usr/local/bin, thus, no PATH
modification is required to use.
LAST version 1047
http://last.cbrc.jp/
LAST finds similar regions between sequences, and aligns them. It is designed for
comparing large datasets to each other (e.g. vertebrate genomes and/or large numbers
of DNA reads).
MACS2 version 2.2.6
http://liulab.dfci.harvard.edu/MACS/
MACS stands for Model-based Analysis of Chip-Seq. It is used to identify
transcript factor biding sites.
MAFFT version 7.450
http://mafft.cbrc.jp/alignment/software/
MAFFT is a multiple sequence alignment program.
It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences),
FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.
Mash version 2.3
https://mash.readthedocs.io/en/latest/
Fast genome and metagenome distance estimation using MinHash.
MaSuRCA version 3.3.6
http://www.genome.umd.edu/masurca.html
MaSuRCA is a whole genome assembly program.
It is installed at /usr/local/masurca. To use:
PATH=/usr/local/masurca/bin:$PATH
Example configuration file is at /usr/local/masurca/sr_config_example.txt. Copy
this file to your own area and modify as needed.
MATLAB version R2022a
http://www.mathworks.com
MATLAB is a programming environment for data analysis, visualization, and numerical computation.
It is installed at /usr/local/MATLAB. To use:
PATH=${PATH}:/usr/local/MATLAB/R2022a/bin
MATLAB, as any other compute intensive task, must be executed on BIOMIX via SLURM batch system.
One way of doing it, is by preparing a MATLAB script that can be executed non-interactively, this is
without MATLAB console. If you must use MATLAB’s interactive interface, submit SLURM interactive
job. Information about SLURM interactive jobs can be found at
http://bioit.dbi.udel.edu/BIOMIX/SLURM-intro.html
Mauve version 2.4
http://darlinglab.org/mauve/mauve.html
Mauve is a tool for performing multiple genome alignments in the presence of large-scale
evolutionary events such as rearrangement and inversion. It is installed at /usr/local/mauve.
The GUI requires old version of Java to work. Such old version is present on the master node
of the BIOMIX cluster only. So, this is the only location where you could execute Mauve GUI.
Since you cannot execute anything resource intensive on the master node, the GUI may be of
limited use to you. To start the GUI:
PATH=$PATH:/usr/local/mauve
followed by mauve.
There is a command line version of Mauve aligner. It doesn't use Java, and it works on all cluster nodes,
and, thus, it may be a better option for you. To use command line aligner:
PATH=$PATH:/usr/local/mauve/linux-x64/
Next type mauveAligner to see program's options.
MaxBin version 2.2.5
https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html
MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.
It is installed at /usr/local/MaxBin. To use:
PATH=$PATH:/usr/local/MaxBin
Medaka version 1.4.3
https://github.com/nanoporetech/medaka
Mmedaka is a tool to create consensus sequences and variant calls from nanopore sequencing data.
MAGA version 11
https://www.megasoftware.net/
MEGA (Molecular Evolutionary Genetics Analysis) software contains a large collection of methods and tools of computational molecular evolution.
MEGA11 has new additions that make MEGA a more comprehensive tool for building timetrees of species, pathogens,
and gene families using rapid relaxed-clock methods.
Find more details on how to use megacc (MEGA in command-line mode) from (some examples at /usr/local/megacc/Examples/):
https://www.megasoftware.net/web_help_11/Running_in_Command-Line_Mode.htm
https://www.megasoftware.net/web_help_10/Quick_Start_Tutorial.htm
Command-line version of MEGA11 is installed at /usr/bin/megacc
MEGAHIT version 1.2.9
https://github.com/voutcn/megahit
MEGAHIT is an ultra-fast tool for large and complex metagenomics assembly via succinct de Bruijn graph.
MEGAN6 version 6.18.4
http://ab.inf.uni-tuebingen.de/software/megan6/
MEGAN6 is a comprehensive toolbox for analysis of microbiome data. All the interactive tools you need in one application.
Type MEGAN to launch.
MEME version 5.1.1
http://meme-suite.org/
The MEME suite provides motif-based sequence analysis tools. It is installed at /usr/local/meme. To use:
PATH=$PATH:/usr/local/meme/bin:/usr/local/meme/libexec/meme-5.1.1
T-Gene, GOMo, and Motif databases are installed at /usr/local/meme/tgene_databases, /usr/local/meme/gomo_databases, and
/usr/local/meme/motif_databases.
MetaBAT version 2.15.3
https://bitbucket.org/berkeleylab/metabat
MetaBAT is automated metagenome binning software, which integrates empirical probabilistic distances of genome
abundance and tetranucleotide frequency. It is installed at /usr/local/metabat. To use:
PATH=$PATH:/usr/local/metabat/bin
METABOLIC version 4.0
https://github.com/AnantharamanLab/METABOLIC/wiki
METabolic And BiogeOchemistry anaLyses In miCrobes
This software enables the prediction of metabolic and biogeochemical functional trait profiles to any given genome datasets.
These genome datasets can either be metagenome-assembled genomes (MAGs), single-cell amplified genomes (SAGs) or isolated
strain sequenced genomes. METABOLIC has two main implementations, which are METABOLIC-G and METABOLIC-C.
They are installed at /usr/local/METABOLIC/.
MetaEuk
https://github.com/soedinglab/metaeuk
MetaEuk is a gene discovery and annotation tool for large-scale eukaryotic metagenomics.
MetaVelvet version 1.2.01
http://metavelvet.dna.bio.keio.ac.jp/
MetaVelvet is a de novo metagenome assembler from short sequence reads.
MG-RAST Tools
https://github.com/MG-RAST/MG-RAST-Tools
MG-RAST provides Science as a Service for environmental DNA (“metagenomic sequences”) at https://mg-rast.org
MG-RAST Tools is a repository of scripts and libraries for using the MG-RAST API and MG-RAST data.
It is installed at /usr/local/MG-RAST-Tools. To use:
export PERL5LIB=$PERL5LIB:/usr/local/MG-RAST-Tools/mglib
Minimap2 version 2.22 (r1101)
https://github.com/lh3/minimap2/
Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database.
MIRA version 4.0.2
http://www.chevreux.org/projects_mira.html
MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454,
Solexa (Illumina), IonTorrent data and PacBio (the later at the moment only
CCS and error-corrected CLR reads). It is installed at /usr/local/mira.
To use:
PATH=$PATH:/usr/local/mira/bin
miRDeep2 version 0.1.3
https://www.mdc-berlin.de/8551903/en/
miRDeep2 helps to sciver microRNA genes by analyzing sequences RNAs. It is located
at /usr/local/mirdeep2. To use:
source /usr/local/mirdeep2/bashrc
Mothur version 1.48.0
http://www.mothur.org/
The goal of Mothur is to have a single software to provide a complete set of tools to analyze molecular
data that ared used by microbial ecologists. It is installed at /usr/local/mothur. To use:
PATH=/usr/local/mothur:$PATH
MMseqs2 version 14-7e284
https://github.com/soedinglab/MMseqs2
MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and
nucleotide sequence sets.
It is installed at /usr/local/mmseqs. To use:
PATH=$PATH:/usr/local/mmseqs/bin
MultiQC version 1.27.1
https://multiqc.info/
MultiQC is a tool to create a single report with interactive plots for multiple bioinformatics analyses across many samples.
Reports are generated by scanning given directories for recognised log files. These are parsed and a single HTML report
is generated summarising the statistics for all logs found. MultiQC reports can describe multiple analysis steps and large
numbers of samples within a single plot, and multiple analysis tools making it ideal for routine fast quality control.
A very large number of Bioinformatics tools are supported by MultiQC. Please see the MultiQC website for a complete list.
MUMmer version 4.0.0.rc1
https://github.com/mummer4/mummer/releases/
MUMmer provides tools for rapid alignment of entire genomes, whether in complete or draft form.
The latest version 4 is installed at /usr/local/bin/.
Note: mapview is not available from the new MUMmer4 installation, but can be accessed from the older version 3
http://mummer.sourceforge.net/ ,
which is installed at /usr/local/MUMmer. To use:
PATH=$PATH:/usr/local/MUMmer
MUSCLE version 3.8.31
http://www.drive5.com/muscle/
MUSCLE is a very fast program for multiple sequence alignment.
Nanopolish version 0.13.3
https://github.com/jts/nanopolish
Software package for signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an
improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels
with respect to a reference genome and more.
It is installed at /usr/local/nanopolish. To use:
PATH=$PATH:/usr/local/nanopolish
NCBI BLAST+ version 2.13.0
http://blast.ncbi.nlm.nih.gov/
The Basic Local Alignment Search Tool (BLAST) finds regions oflocal similarity
between sequences. The program compares nucleotide or proteinsequences to
sequence databases and calculates the statistical significance of matches.
NCBI C++ Toolkit version 22
https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/
It is installed at /usr/local/ncbi-toolkit. To use its compiled binaries and scripts:
PATH=$PATH:/usr/local/ncbi-toolkit/bin
OrthoFinder
OrthoFinder version 2.3.1
https://github.com/davidemms/OrthoFinder
OrthoFinder is a comprehensive tool for comparative genomics. It finds orthologs and orthogroups, infers
rooted gene trees for all orthogroups and identifies all of the gene duplication events in those gene trees.
It is installed at /usr/local/OrthoFinder. To use:
PATH=$PATH:/usr/local/OrthoFinder
OrthoFinder version 3.1.0
https://github.com/OrthoFinder/OrthoFinder
It is installed at /opt/anaconda3/envs/of3_env/. To use:
unset -f conda
export PATH=/opt/anaconda3/bin:$PATH
source /opt/anaconda3/etc/profile.d/conda.sh
conda activate of3_env
PacBio SMRT Tools version 25.1.0
PacBio SMRT Link command tools (SMRT Tools) are installed at /usr/local/smrtlink. With these
tools, you can use BIOMIX cluster to process PacBio sequencing data. Consult PacBio
documentation on the use of the tools -
https://www.pacb.com/wp-content/uploads/SMRT-Link-User-Guide-v25.1.pdf
To use, set up the following variables:
SMRT_ROOT=/usr/local/smrtlink/
PATH=$SMRT_ROOT/smrtcmds/bin:$PATH
PacBio Tools
A number of auxiliary PacBio Tools are installed via pitchfork
at /usr/local/pitchork. They include blasr, bax2bam and a few more. To use:
source /usr/local/pitchfork/deployment/setup-env.sh
If a PacBio tool or a library, that you need, is not there, send me a note (miaskiew@udel.edu),
and I'll try to install it.
PartitionFinder2 version 2.1.1
http://www.robertlanfear.com/partitionfinder/
PartitionFinder is a tool to select best-fit partitioning schemes and models of molecular
evolution for phylogenetic analyses.
It is installed at /usr/local/partitionfinder. To use:
alias python=/usr/bin/python2 (PartitionFinder does not work with Python3)
python /usr/local/partitionfinder/PartitionFinder.py (followed by required arguments)
Phylosift version 1.0.1
https://phylosift.wordpress.com/
PhyloSift is a suite of software tools to conduct phylogenetic analysis of genomes and metagenomes.
It is installed at /usr/local/phylosift. To use:
export PATH=$PATH:/usr/local/phylosift/bin
Pindel version 0.2.4w
http://gmt.genome.wustl.edu/packages/pindel/
Pindel can detect breakpoints of large deletions, medium sized insertions, inversions,
tandem duplications and other structural variants at single-based resolution from
next-gen sequence data.
Picard Tools version 3.0.0
http://broadinstitute.github.io/picard/
Picard provide a set of command line tools for manipulating high-throughput sequencing (HTS)
data and formats such as SAM/BAM/CRAM and VCF. It is installed at /usr/local/picard-tools.
To use:
java -jar /usr/local/picard-tools/picard.jar -h
Pilon version 1.23
https://github.com/broadinstitute/pilon/wiki
Pilon is a software tool which can be used to:
-- automatically improve draft assemblies
-- find variation among strains, including large event detection
Pilon version 1.23 introduces two new arguments to specify long read input BAMs:
--nanopore ont.bam identifies ont.bam as containing long reads from Oxford Nanopore sequencing
--pacbio pb.bam identifies pb.bam as containing long reads from Pacific Biosciences sequencing
Pilon Java jar file is installed as /usr/local/pilon.jar, so:
java -jar /usr/local/pilon.jar
PLINK version 1.07
http://zzz.bwh.harvard.edu/plink/
PLINK is a whole genome association analysis toolset, designed to perform a range of basic,
large-scale analyses in a computationally efficient manner.
To use:
plink --noweb
PLINK version 1.90 beta
https://www.cog-genomics.org/plink/1.9/general_usage
This is a comprehensive update to Shaun Purcell's PLINK command-line program, developed by Christopher
Chang with support from the NIH-NIDDK's Laboratory of Biological Modeling, the Purcell Lab, and others.
It is installed at :
/usr/local/plink-1.90beta/plink
Porechop version 0.2.4
https://github.com/rrwick/Porechop
Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are
trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads.
(Porechop is officially unsupported since October 2018.)
Pplacer version 1.1alpha19
http://matsen.fhcrc.org/pplacer
Pplacer places query sequences on a fixed reference phylogenetic tree to
maximize phylogenetic likelihood or posterior probability according to a
reference alignment.
It is installed in /usr/local/pplacer. To use:
PATH=$PATH:/usr/local/pplacer/bin:/usr/local/pplacer/scripts
Prank version 170427
http://wasabiapp.org/software/prank/
PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. It is installed at /usr/local/prank. To use:
PATH=$PATH:/usr/local/prank/bin
Prodigal version 2.6.3
https://github.com/hyattpd/Prodigal
Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a
microbial (bacterial and archaeal) gene finding program.
Prokka version 1.14.5
https://github.com/tseemann/prokka
Prokka is a software tool to annotate bacterial, archaeal and viral genomes quickly and produce
standards-compliant output files.
It is installed at /usr/local/prokka. To use:
PATH=$PATH:/usr/local/prokka/bin
Pullseq version 1.0.2
https://github.com/bcthomas/pullseq
Pullseq extracts sequences from a fasta/fastq file. It is fast, and can be useful in a variety of situations.
You can use it to extract sequences from one fasta/fastq file into a new file, given either a list of header
ids to include or a regular expression pattern to match. Results can additionally be filtered with
minimum/maximum sequence lengths. Pullseq can laso convert from fastq to fasta or visa-versa and can change
the length of the output sequence lines.
Pysam version 0.15.4
https://github.com/pysam-developers/pysam
Pysam is a python module for reading and manipulating SAM/BAM files.
Quast version 5.2.0
https://github.com/ablab/quast
QUAST evaluates genome assemblies by computing various metrics.
QIIME 2 version 2.0
https://qiime2.org
QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package. QIIME 2 enables researchers
to start an analysis with raw DNA sequence data and finish with publication-quality figures and statistical
results.
QIIME 2 is a complete redesign and rewrite of the QIIME 1 microbiome analysis pipeline.
QIIME 2 addresses many of the limitations of QIIME 1, while retaining the features that made QIIME 1 a
powerful and widely-used analysis pipeline.
QIIME 2 installation is 100% in user space using miniconda. Follow directions posted at
https://docs.qiime2.org/2023.5/install/native/
to get QIIME 2 installed and working for you.
R with Bioconductor version 3.6.2
https://www.r-project.org/
https://www.bioconductor.org/
R is a free software environment for statistical computing and graphics.
Bioconductor provides tools for the analysis and comprehension of high-throughput genomic
data in the R environment.
RAxML version 8.2.12
http://sco.h-its.org/exelixis/web/software/raxml
RAxML - Randomized Axelerated Maximum Likelihood - is a tool for phylogenetic
analysis and post-analysis of large phylogenies. Serial (not parallel)
executable is called raxml. Multi-threaded (parallel) executable is called
raxml-pthreads.
If you want to use auxiliary scripts that are distributed with RAxML, set up the PATH
to include /usr/local/raxml/usefulScripts:
PATH=$PATH:/usr/local/raxml/usefulScripts
RDP Classifier version 12
http://rdp.cme.msu.edu/
The RDP Classifier can rapidly and accurately classify bacterial and archaeal 16s rRNA
sequences, Fungal LSU and ITS sequences. It provides taxonomic assignments from domain
to genus, with confidence estimates for each assignment. It is installed at
/usr/local/rdp_classifier. To use:
java -Xmx1g -jar /usr/local/rdp_classifier/dist/classifier.jar
Regenie version 2.0.2
https://rgcgithub.github.io/regenie/
Regenie can be used for whole genome regression modelling of large genome-wide association studies.
Roary version 3.13.0
https://sanger-pathogens.github.io/Roary/
Roary is a pan genome pipeline, which takes annotated assemblies in GFF3 format
(produced by Prokka) and calculates the pan genome. It is installed at /usr/local/Roary.
To use:
export PATH=$PATH:/usr/local/Roary/bin
export PERL5LIB=$PERL5LIB:/usr/local/Roary/lib
In addition, programs, on which Roary scripts depend, must be in your PATH.
RSEM version 1.3.2
http://deweylab.github.io/RSEM/
RSEM is an RNA-Seq transcript quantification program. It is installed at /usr/local/RSEM.
To use append PATH:
PATH=$PATH:/usr/local/RSEM
RSeQC version 5.0.4
http://rseqc.sourceforge.net/
RSeQC package provides a number of useful modules that can comprehensively evaluate high
throughput sequence data especially RNA-seq data. Some basic modules quickly inspect
sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific
modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity,
strand specificity, transcript level RNA integrity etc.
RStudio version 2023.03.0 Build 386
https://www.rstudio.com/
RStudio provides graphical user interface to R. It is installed under /usr/local/rstudio.
To run RStudio on Biomix, you have to ssh to biomix with X11 forwarding. Next, you should submit an
interactive SLURM job with X11 forwarding, as described in the document
Introduction to SLURM. After this, you could launch the program by
typing:
/usr/local/rstudio/rstudio
Salmon version 1.1.0
https://github.com/COMBINE-lab/salmon
Salmon is a very fast program to produce a highly-accurate, transcript-level quantification
estimates from RNA-seq data. It is installed at /usr/local/salmon. To use:
PATH=$PATH:/usr/local/salmon/bin
Sambamba version 0.7.1
http://lomereiter.github.io/sambamba
Fast tools for working with SAM/BAM files (view, sort, index, merge, slice, markdup, flagstat).
SAMtools version 0.1.19
http://samtools.sourceforge.net/
SAM Tools provide various utilities for manipulating alignments in the SAM
format, including sorting, merging, indexing and generating alignments in
a per-position format.
While new 1.x release of SAMtools and BCFtools is available, older 0.1.19
version of SAMtools is required by quite a few other software packages to
work.
SAMtools version 1.19.2
http://www.htslib.org/
Samtools is a suite of programs for interacting with high-throughput
sequencing data.
There are 2 versions of SAMtools installed: this version, and version 0.1.19
(see previous paragraph).
This version 1.19.2 is installed at /usr/local/bin, while version 0.1.19 is
installed at /usr/bin.
/usr/local/bin should preceed /usr/bin in your PATH, so simply typing "samtools"
should launch version 1.19.2. However, if your PATH is modified and /usr/bin
is ahead of /usr/local/bin, "samtools" will start the old version. It this is
not what you want, you need to adjust/rearrange the PATH accordingly, or you
could call samtools with the full path, such as /usr/local/bin/samtools.
SeqKit version 0.11.0
https://github.com/shenwei356/seqkit
SeqKit is a very fast toolkit for manipulations of FASTA and FASTQ files: converting,
searching, filtering, deduplication, splitting, shuffling, and sampling.
SMARTdenovo
https://github.com/ruanjue/smartdenovo
SMARTdenovo is a de novo assembler for PacBio and Oxford Nanopore (ONT) data. It produces an assembly from
all-vs-all raw read alignments without an error correction stage. It also provides tools to generate accurate
consensus sequences, though a platform dependent consensus polish tools (e.g. Quiver for PacBio or Nanopolish
for ONT) are still required for higher accuracy.
SMARTdenovo consists of five separate modules / command line tools: wtzmo for read overlapping, wtgbo to rescue
missing overlaps, wtclp for identifying low-quality regions and chimaera, and wtcns or wtmsa to produce better
unitig consensus. The smartdenovo.pl script provides a convenient interface to call these programs in one go.
SMARTdenovo is installed at /usr/local/smartdenovo.
snpEff version 5.2c
https://pcingola.github.io/SnpEff/
Genetic variant annotation, and functional effect prediction toolbox. It annotates and predicts the effects of
genetic variants on genes and proteins (such as amino acid changes).
You could find the program at :
/usr/local/snpEff/
Sniffles version 1.0.11
https://github.com/fritzsedlazeck/Sniffles
Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore).
It detects all types of SVs using evidence from split-read alignments, high-mismatch regions, and
coverage analysis.
SOAPdenovo2 version 2.04-r241
https://github.com/aquaskyline/SOAPdenovo2
SOAPdenovo is a novel short-read assembly method that can build a de novo
draft assembly for the human-sized genomes. The program is specially designed
to assemble Illumina GA short reads. SOAPdenovo is installed at
/usr/local/SOAPdenovo2. There are two executables in this location: SOAPdenovo-63mer,
and SOAPdenovo-127mer. To use:
PATH=$PATH:/usr/local/SOAPdenovo2
Note that program MEGAHIT, available on BIOMIX, is the formal successor of SOAPdenovo2.
SPAdes
About SPAdes
SPAdes is a versatile toolkit designed for assembly and analysis of sequencing data. SPAdes is primarily developed for Illumina sequencing data, but can be used for IonTorrent as well. Most of SPAdes pipelines support hybrid mode, i.e. allow using long reads (PacBio and Oxford Nanopore) as a supplementary data.
The version 3.15.5 was installed previously and still available.
The latest version SPAdes 4.0.0 has been installed (see SPAdes releases ).
It is installed at /usr/local/SPAdes. To use:
PATH=$PATH:/usr/local/SPAdes/bin
Spaln version 3.0.6c
https://github.com/ogotoh/spaln
Map and align a set of cDNA/EST or protein sequences onto a genome.
Spaln is installed at /usr/local/bin, and you should not need any configuration to start
the program. However, if you need to prepare "seqdb" directory (see spaln documentation):
cp /usr/local/spaln/seqdb-orig ~/seqdb
cd ~/seqdb (and format your sequence per documentation)
SRA Toolkit version 3.0.1
https://github.com/ncbi/sra-tools
The SRA Toolkit from NCBI is a collection of tools and libraries for using data in the INSDC
Sequence Read Archives (SRA format). To use:
source /usr/local/ncbi/sra-tools.sh
STAR version 2.7.11b
https://github.com/alexdobin/STAR
Spliced Transcripts Alignment to a Reference (STAR) software performs accurate alignment
of high-throughput RNA-seq sequencing data.
There are two versions of the program available: STAR and STARlong. STARlong version uses a more efficient
seed stitching algorithm for long reads.
StringTie version 3.0.0
https://ccb.jhu.edu/software/stringtie/
StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.
Tandem Repeats Finder (TRF) version 4.09
https://tandem.bu.edu/trf/trf.html
A tandem repeat in DNA is two or more adjacent, approximate copies of a pattern of
nucleotides. Tandem Repeats Finder is a program to locate and display tandem repeats
in DNA sequences.
TopHat version 2.1.1
http://ccb.jhu.edu/software/tophat
TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads
to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie,
and then analyzes the mapping results to identify splice junctions between exons.
Trim Galore version 0.6.6
http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
A Perl wrapper tool around Cutadapt and FastQC to consistently apply quality
and adapter trimming to FastQ files. Type trim_galore (with required arguments) to launch
the program.
Trimmmomatic version 0.39
http://www.usadellab.org/cms/?page=trimmomatic
A flexible read trimming tool for Illumina NGS data.
It is installed at /usr/local/Trimmomatic. To use:
java -jar /usr/local/Trimmomatic/trimmomatic.jar
Trinity version 2.9.1
https://github.com/trinityrnaseq/trinityrnaseq/wiki
Trinity assembles transcript sequences from Illumina RNA-Seq data. It is
installed at /usr/local/trinityrnaseq.
To use:
export PATH=$PATH:/usr/local/bowtie2:/usr/local/trinityrnaseq
Usearch version 11.0 and Uclust version 1.2.21
http://www.drive5.com/usearch/
These are tools for high-throughput search and clustering. Note, that only 32-bit
version of usearch is freely available and this what is installed on Biomix. This version of usearch
is limited to 4GB of RAM, and 8 cores.
VarScan version 2.4.3
http://dkoboldt.github.io/varscan/
Variant detection tool. It is installed at /usr/local/VarScan.jar. To run:
java -jar /usr/local/VarScan.jar
Vcftools version 0.1.16.4
https://vcftools.github.io/
Vcftools provide utilities to work with the variant call format (VCF) and
binary variant call format (BCF) files.
Velvet version 1.2.10
http://www.ebi.ac.uk/~zerbino/velvet/
Velvet is a sequence assembler for very short reads.
Vmatch version 2.3.1
http://www.vmatch.de/
Vmatch is a software tool for efficiently solving large scale sequence matching tasks.
It is installed at /usr/local/vmatch. To use:
PATH=$PATH:/usr/local/vmatch
VSEARCH version 2.17.1
https://github.com/torognes/vsearch
VSEARCH supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication,
rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment
searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering, conversion and
merging of paired-end reads.
It is an alternative to the Usearch tool, which free use is limited to a 32-bit version only.
Wise2 version 2.4.1
http://www.ebi.ac.uk/~birney/wise2/
The key program of the Wise2 package is genewise which performs aligining
proteins HMMs to DNA.
Xenium Ranger version 3.1.1
https://www.10xgenomics.com/support/software/xenium-ranger/latest
What is Xenium Ranger?
The Xenium In Situ software suite is a set of software applications for analyzing and visualizing in situ gene expression data produced by the Xenium Analyzer. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells, import your own segmentation data, or rename datasets.
To use:
export PATH=/usr/local/xeniumranger-xenium3.1.1:$PATH