The following is a partial list of software tools available on the cluster. If you want to know exactly which modules are available on the cluster, type module avail in the command line.
To use the tools listed below, type the command module load <module_name>, where <module_name> is the name that appear in the middle column of each table below.
See this wiki page for more information on software modules and the module command.
|
Software Name |
Module Name |
Description |
| Athena++ | athenapp | A complete re-write of the Athena astrophysical magnetohydrodynamics (MHD) code in C++ |
|
Software Name |
Module Name |
Description |
| Bamtools | bamtools | BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files |
| bcl2fastq | bcl2fastq | A quantitative proteomics software package designed for analyzing large mass-spectrometric data sets |
| Bcftools | bcftools | A set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF |
| bedgraphToBigwig | bedgraphtobigwig | Convert a bedGraph file to bigWig format |
| Bedops | bedops | High-performance genomic feature operations |
| Bedtools | bedtools | A swiss-army knife of tools for a wide-range of genomics analysis tasks |
| Bioawk | bioawk |
Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It also adds a few built-in functions and an command line option to use TAB as the input/output delimiter. When the new functionality is not used, bioawk is intended to behave exactly the same as the original BWK awk. The original awk requires a YACC-compatible parser generator (e.g. Byacc or Bison). Bioawk further depends on zlib so as to work with gzip'd files. |
| Biscuit | biscuit | A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data |
| Bismark | bismark | A tool to map bisulfite converted sequence reads and determine cytosine methylation states |
| Blast | blast | A suite of BLAST tools that utilizes the NCBI C++ Toolkit. To download Blast databases from command line see this link. |
| BLAT | blat | A bioinformatics software tool which performs rapid mRNA/DNA and cross-species protein alignments |
| Bowtie1 | bowtie1 | An ultrafast, memory-efficient short read aligner |
| Bowtie2 | bowtie2 | An ultra fast and memory-efficient tool for aligning sequencing reads to long reference sequences |
| Busco | busco | BUSCO is a tool to assess completeness of genome assembly, gene set and transcriptome. It is based on the concept of single-copy orthologs that should be highly conserved among the closely related species. |
| BWA | BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome. It consists of three algorithms: BWA-backtrack, BWA-SW and BWA-ME | |
| CD-Hit | cd-hit | Clusters and compares protein or nucleotide sequences |
| Cellranger | cellranger | A set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more |
| Chimerax | chimerax | The next-generation molecular visualization program |
| Cufflinks | cufflinks | Assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples |
| Cutadapt | cutadapt | Trim adapters from high-throughput sequencing reads |
| dcm2niix | dcm2niix | Convert neuroimaging data from the DICOM format to the NIfTI format |
| DeepLabCut | deeplabcut | DeepLabCut is a toolbox for markerless pose estimation of animals performing various tasks. |
| Deeptools | deeptools | DeepTools addresses the challenge of handling the large amounts of data that are now routinely generated from DNA sequencing centers |
| Diamond | diamond | A sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data |
| Eman2 | eman2 | EMAN2 is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes. EMAN's original purpose was performing single particle reconstructions (3-D volumetric models from 2-D cryo-EM images) at the highest possible resolution, but the suite now also offers support for single particle cryo-ET, and tools useful in many other subdisciplines such as helical reconstruction, 2-D crystallography and whole-cell tomography. EMAN2 is capable of processing large data sets (>100,000 particle) very efficiently. |
| EIGENSOFT | EIG | The package implements methods for analzing population structure and performing stratification correction |
| Epic2 | epic2 | Ultra performant Chip-Seq broad domain finder based on SICER module |
| FastANI | fastani | FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). |
| FastQC | fastqc | A quality control tool for high throughput sequence data |
| FastQTL | fastqtl | QTL mapping software |
| Fastx Toolkit | fastx_toolkit | A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing |
| Gatk | gatk4 | Genome Analysis Toolkit. Variant Discovery in High-Throughput Sequencing Data |
| GffRead | gffread | The program can be used to validate, filter, convert and perform various other operations on GFF files |
| ggsashimi | ggsashimi | Command-line tool for the visualization of splicing events across multiple samples |
| Gimmemotifs | gimme | Motif prediction pipeline and various motif-related tools |
| Grand Slam | grandslam | A computational approach to infer the proportion and the corresponding posterior distribution of new and old RNA for each gene from SLAM-seq experiments |
| Hi-C User Pipeline | HiCUP | A tool for mapping and performing quality control on Hi-C data |
| Hic-Pro | hic-pro | An optimized and flexible pipeline for Hi-C data processing |
| Hisat2 | hisat2 | Graph-based alignment of next generation sequencing reads to a population of genomes |
| Homer | homer | Hypergeometric Optimization of Motif EnRichment is a suite of tools for Motif Discovery and next-gen sequencing analysis |
| HRIBO | hribo | HRIBO (High-throughput annotation by Ribo-seq), a workflow to enable reproducible and high-throughput analysis of bacterial Ribo-seq data |
| HTSeq | htseq | A Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments |
| IGV | igv | A high-performance, easy-to-use, interactive tool for the visual exploration of genomic data |
| Juicer | juicer | Juicer is a platform for analyzing kilobase resolution Hi-C data. In this distribution, we include the pipeline for generating Hi-C maps from fastq raw data files and command line tools for feature annotation on the Hi-C maps. |
| Macs | macs | Model-based Analysis for ChIP-Seq |
| MaxQuant | maxquant | A quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. License restricted |
| MAKER | maker | Maker is a portable and easily configurable genome annotation pipeline module |
| MEME | meme | The MEME Suite consists of several command line programs and an optional web server. Building and installing the command line programs is very straight-forward. See the 'Quick Install' link below to get started. |
| Megalodon | megalodon | A research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transcriptome |
| MethylDackel | methyldackel | A (mostly) universal methylation extractor for BS-seq experiments. Formerly named PileOMeth |
| MultiQC | multiqc | Create aggregate bioinformatics analysis reports across many samples and tools |
| Mirdeep | Mirdeep2 | A completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs |
| MitoZ | mitoz | MitoZ is a Python3-based toolkit which aims to automatically filter pair-end raw data (fastq files), assemble genome, search for mitogenome sequences from the genome assembly result, annotate mitogenome (genbank file as result), and mitogenome visualization. |
| NucDiff | nucdiff | Locates and categorizes differences between two closely related nucleotide sequences |
| OrthoFinder | orthofinder | OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics |
| Pangolin | pangolin | Pangolin was developed to implement the dynamic nomenclature of SARS-CoV-2 lineages, known as the Pango nomenclature. It allows a user to assign a SARS-CoV-2 genome sequence the most likely lineage (Pango lineage) to SARS-CoV-2 query sequences. |
| Pear | pear | An ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory. |
| Pgap | pgap | The NCBI Prokaryotic Genome Annotation Pipeline is designed to annotate bacterial and archaeal genomes (chromosomes and plasmids) |
| Phyluce | phyluce | For analyzing both data collected from UCE loci and also data collection from other types of loci for phylogenomic studies at the species, population, and individual levels |
| PhyML | phyml | PhyML is a software that estimates maximum likelihood phylogenies from alignments of nucleotide or amino acid sequences |
| Picard | picard | A set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF |
| Plink 1 | plink | Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner |
| Plink 2 | plink2 | Whole genome association analysis toolset |
| Picrust2 | picrust2 | Phylogenetic Investigation of Communities by Reconstruction of Unobserved States is a software for predicting functional abundances based only on marker gene sequences |
| Portal Client | portal_client | Python-based client for downloading data files hosted by the an instance of the portal software developed by the GDC and further modified by the Institute for Genome Sciences (IGS) |
| QIIME2 | qiime2 | A next-generation microbiome bioinformatics platform. The software is installed as a container. Use the command $QIIME2 instead of qiime. |
| RepeatModeler | repeatmodeler | is a de-novo repeat family identification and modeling package |
| rMATS | rmats | rMATS is a computational tool to detect differential alternative splicing events from RNA-Seq data |
| rmats2sashimiplot | rmats | Produces a sashimiplot visualization of rMATS output. Included in rMATS installation. |
| Rsem | rsem | RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data |
| Samtools | samtools | Tools for dealing with SAM, BAM and CRAM files |
| Salmon | salmon | Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment |
| ScanExitron | scanexitron | A computational workflow for exitron splicing identification |
| Snakemake | snakemake | Workflow management system tool to create reproducible and scalable data analyses |
| Space Ranger | spaceranger | Visium Spatial Gene Expression is a next-generation molecular profiling solution for classifying tissue based on total mRNA. Space Ranger is a set of analysis pipelines that process Visium Spatial Gene Expression data with brightfield and fluorescence microscope images |
| SraToolkit | sratoolkit | A set of tools that download, manipulate and validate next-generation sequencing data stored in the NCBI SRA archive. Before first use follow instructions here. |
| Stacks | stacks | Stacks is a software pipeline for building loci from RAD-seq |
| Statsmodels | statsmodels | A Python module that provides classes and functions for the estimation of many different statistical models, as well as for conducting statistical tests, and statistical data exploration |
| STAR | STAR | Ultra fast universal RNA-seq aligner |
| StringTie | stringtie | A fast and highly efficient assembler of RNA-Seq alignments into potential transcripts |
| Subread | subread | High-performance read alignment, quantification, and mutation discovery |
| Tobias | tobias | Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal |
| Tophat | tophat | A spliced read mapper for RNA-Seq |
| Trim Galore | trim-galore | A wrapper script to automate quality and adapter trimming as well as quality control |
| Trinity | trinity | assembles transcript sequences from Illumina RNA-Seq data |
| Ultraplex | ultraplex | Ultraplex is an all-in-one software package for processing and demultiplexing fastq files |
| UMI-tools | umitools | Tools for dealing with Unique Molecular Identifiers (UMIs) / Random Molecular Tags (RMTs) |
| Uropa | uropa | UROPA (Universal RObust Peak Annotator) is a command line based tool, intended for genomic region annotation from e.g. peak calling. It detects the most appropriate annotation by taking parameters such as feature type, anchor, direction and strand into account. Furthermore, it allows filtering for GTF attribute values, e.g. protein_coding. |
| Vast-Tools | vast-tools | Vertebrate Alternative Splicing and Transcription Tools (VAST-TOOLS) is a toolset for profiling and comparing alternative splicing events in RNA-Seq data |
| Vcftools | vcftools | A set of tools written in Perl and C++ for working with VCF files. This package only contains the C++ libraries whereas the package perl-vcftools-vcf contains the perl libraries |
| Vienna RNA | viennarna | RNA secondary structure prediction and comparison |
| Trimmomatic | trimmomatic | A flexible read trimming tool for Illumina NGS data |
| Software Name | Module Name | Description |
| BAGEL | bagel | A parallel electronic-structure program |
| Software Name | Module Name | Description |
| WRF | wrf | The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs |
| Software Name | Module Name | Description |
| CIS | cis | An open source Python library and command-line tool for the easy collocation, visualization, analysis, and comparison of a diverse set of gridded and ungridded datasets used across earth sciences |
|
Software Name |
Module Name |
Description |
| Aspera CLI | ascli | Command Line Interface for IBM Aspera products |
| aria2 | aria2 | A lightweight multi-protocol & multi-source command-line download utility |
| IBAMR | ibamr | A distributed-memory parallel implementation of the immersed boundary (IB) method with support for Cartesian grid adaptive mesh refinement (AMR) |
| GDL | gdl | GDL is a free/libre/open source incremental compiler compatible with IDL (Interactive Data Language) and to some extent with PV-WAVE. Together with its library routines it serves as a tool for data analysis and visualization in such disciplines as astronomy, geosciences and medical imaging. |
| NcFTP | ncftp | NcFTP Client (also known as just NcFTP) is a set of FREE application programs implementing the File Transfer Protocol (FTP) |
| OpenFoam | openfoam | OpenFOAM is the free, open source CFD software developed primarily by OpenCFD. It has a large user base across most areas of engineering and science, from both commercial and academic organisations. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to acoustics, solid mechanics and electromagnetics |
| Pyega3 | pyega3 | The pyEGA3 download client is a python-based tool for viewing and downloading files from authorized EGA datasets. |
| Rclone | rclone | A command line program to manage files on cloud storage |
|
Software Name |
Module Name |
Description |
| Connectome Workbench | connectomewb | Visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project |
| FSL | fsl | A comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data |
| FreeSurfer | freesurfer | Neuroimaging toolkit for processing, analyzing, and visualizing human brain MR images |
| Language Name | Module Name | Description |
| Julia | julia | Julia provides asynchronous I/O, metaprogramming, debugging, logging, profiling, a package manager, and more |
| R | R4 | R is a free software environment for statistical computing and graphics |