Anaconda is a freemium open source distribution of the Python and R programming languages for large-scale data processing, predictive analytics, and scientific computing, that aims to simplify package management and deployment.
A tool for accurate dissection of genome-wide allele-specific copy number in tumors.
High-performance transfer plug-in
A data warehouse for integrative bioinformatics
Utilities for variant calling and manipulating VCFs and BCFs
Beagle is a software package that performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection.
A software suite for the comparison, manipulation and annotation of genomic features in browser extensible data (BED) and general feature format (GFF) format.
Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step.
A bisulfite space genotyper & methylation caller
Basic Local Alignment Search Tool
Boost provides free portable peer-reviewed C++ libraries. The emphasis is on portable libraries which work well with the C++ Standard Library.
An ultrafast, memory-efficient short read aligner.
Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
A Perl/C++ package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads.
A wrapper for bowtie to produce small RNA-seq alignments where multimapped small RNAs tend to be placed near regions of confidently high density.
BVATools -- Bam and Variant Analysis Tools
A software package for mapping low-divergent sequences against a large reference genome, such as the human genome.
Bwakit is a self-consistent installation-free package of scripts and precompiled binaries, providing an end-to-end solution to read mapping.
CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.
Cell Ranger is a set of analysis pipelines that processes Chromium single cell 3â€™ RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis.
Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.
Duk is a fast, accurate,and memory efficent DNA sequence matching tool. It finds whether a query sequence partially or totally matches given reference sequences or not, but it does not give how a query matches a reference sequence. The common application is to group sequencing reads into small manageable chunks for downstream analysis in assessing quality of a sequencing run, which includes contaminant removal (with contaminant sequences known), organelle genome separation, and assembly refinement.
A command-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc.
EMBOSS is 'The European Molecular Biology Open Software Suite'. EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community.
A versatile software pipeline to perform various statistical tests for identifying genome-wide association from sequence data through a user-friendly interface, both to scientific analysts and to method developers.
A generic tool for pairwise sequence comparison.
A quality control tool for high throughput sequence data.
FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.
The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
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. FLASH is designed to merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. The resulting longer reads can significantly improve genome assemblies.
The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, Ada, and Go, as well as libraries for theselanguages (libstdc++, libgcj,...). GCC was originally written as the compiler for the GNU operating system.
Flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome.
The GEM library strives to be a true 'next-generation' tool for handling any kind of sequence data, offering state-of-the-art algorithms and data structures specifically tailored to this demanding task.
Genome Analysis Toolkit
Developed by the Data Science and Data Engineering group at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping.
An interpreter for the PostScript language and for PDF.
Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms.
HMMER is used for searching sequence databases for sequence homologs,and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).
HOMER offers tools and methods for interpreting Next-gen-Seq experiments.Â In addition to Genome Browser/UCSC visualization support and peak finding [and motif finding of course], HOMER can help assemble data across multiple experiments and look at positional specific relationships between sequencing tags, motifs, and other features. You do not need to use the peak finding methods in this package to use motif finding.
A C library for reading/writing high-throughput sequencing data
The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets.
The igvtools utility provides a set of tools for pre-processing data files. File names must contain an accepted file extension, e.g. test-xyz.bam.
Java technology is the foundation of most networked applications and is used worldwide to develop and deliver mobile and nested applications, games, web content and enterprise software.
JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA.
UCSC command-line bioinformatic utilities, implemented by Jim Kent
KmerGenie estimates the best k-mer length for genome de novo assembly.
Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.
LAPACK provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems.
Long Ranger is a set of analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants.
Model-based Analysis of ChIP-Seq (MACS) on short reads sequencers such as Genome Analyzer (Illumina / Solexa)
Novel algorithm, named Model-based Analysis of ChIP-Seq (MACS), for identifying transcript factor binding sites.
miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs. The tool reports known and hundreds of novel microRNAs with high accuracy in seven species representing the major animal clades. The low consumption of time and memory combined with user-friendly interactive graphic output makes miRDeep2 accessible for straightforward application in current reasearch.
MPICH is a high performance and widely portable implementation of the Message Passing Interface (MPI) standard.
MUGQIC pipelines consist of Python scripts which create a list of jobs running Bash commands. Those scripts support dependencies between jobs and smart restart mechanism if some jobs fail during pipeline execution. Jobs can be submitted in different ways: by being sent to a PBS scheduler like Torque or by being run as a series of commands in batch through a Bash script
This library implements various -seq downstream analysis, as well as Nozzle-based reporting for mugqic_pipelines.
Perl, python, R, awk and sh scripts use in several bioinfomatics pipelines of the MUGQIC PIPELINE.
Ultra-fast alignment of large-scale DNA and protein sequences
Program for creating multiple alignments of protein sequences.
Reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes
Tool for analysing reads from LMP libraries, generating a comprehensive quality report and extracting good quality trimmed and deduplicated reads
Optimized BLAS library based on GotoBLAS2 1.13 BSD version
Universal document converter
Shell tool for executing jobs in parallel using one or more computers
DRMAA for Torque/PBS Pro is implementation of Open Grid Forum DRMAA (Distributed Resource Management Application API) specification for submission and control jobs to PBS systems
Feature-rich programming language
Set of tools (in Java) for working with next generation sequencing data in the BAM format
Replacement for gzip that exploits multiple processors and multiple cores when compressing data
Used to filter, reformat, or trim your genomic and metagenomic sequence data
Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee.
Programming language that lets you work quickly and integrate systems more effectively
Qualimap is a platform-independent application written in Java and R that provides both a Graphical User Interface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.
face (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data
Parallel genome assemblies for parallel DNA sequencing
Predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA in full genome sequences.
Java program which computes a series of quality control metrics for RNA-seq data
Accurate quantification of gene and isoform expression from RNA-Seq data
A suite of programs for interacting with high-throughput sequencing data.
Software package for detecting INDELs (INsertions and DELetions) mutations in a reference genome
Tool developed to process and analyze small RNA-seq data with respect to a reference genome, and output a comprehensive and informative annotation of all discovered small RNA genes
Predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms
Pacbio secondary analysis through a graphical or command-line user interface.
General purpose gene finding program suitable for both eukaryotic and prokaryotic genomes
Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes
Sphinx is a tool that makes it easy to create intelligent and beautiful documentation of Python projects
SPAdes â€“ St. Petersburg genome assembler â€“ is an assembly toolkit containing various assembly pipelines.
Splicing Adder, a toolbox for alternative splicing analysis based on RNA-Seq alignment data. Briefly, the software takes a given annotation and RNA-Seq read alignments, transforms the annotation into a splicing graph representation, augments the splicing graph with additional information extracted from the read data, extracts alternative splicing events from the graph and quantifies the events.
Spliced Transcripts Alignment to a Reference. Based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure.
Supernova is a software package for de novo assembly from Chromium Linked-Reads that are made from a single whole-genome library from an individual DNA source.
Tabix indexes a TAB-delimited genome position file in.tab.bgz and creates an index file ( in.tab.bgz.tbi or in.tab.bgz.csi ) when region is absent from the command-line.
Predicting Transmembrane Protein Topology with a Hidden Markov Model
Perl, Python, R, awk and sh scripts use in several bioinfomatics pipelines of the MUGQIC PIPELINES repo.
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.
TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks
Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.
Trinity assembles transcript sequences from Illumina RNA-Seq data
A comprehensive annotation suite for functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Trinotate makes use of a number of different well referenced methods for functional annotation including homology search to known sequence data (BLAST+/SwissProt), protein domain identification (HMMER/PFAM), protein signal peptide and transmembrane domain prediction (signalP/tmHMM), and leveraging various annotation databases (eggNOG/GO/Kegg databases).
UCSC genome browser 'kent' bioinformatic utilities
Ultra-fast search for high-identity top hit or hits from sequence files
VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454 and similar instruments. It can be used to detect different types of variation: Germline variants, multi-sample variants, somatic mutations and somatic copy number alterations
A program package that can be used to perform the following operations on standard variants (VCF) files: Filter out specific variantsCompare filesSummarize variantsConvert to different file typesValidate and merge filesCreate intersections and subsets of variants
Verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals), and checks whether the reads are contaminated as a mixture of two samples. verifyBamID can detect sample contamination and swaps when external genotypes are available. When external genotypes are not available, verifyBamID still robustly detects sample swaps
The ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.
VSEARCH supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, 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 and conversion.
A tool set for short variant discovery in genetic sequence data.
A tool for creating sequence logos from biological sequence alignments. It can be run on the command line as a standalone webserver, as a CGI webapp, or as a python library.
A de novo whole-genome shotgun (WGS) DNA sequence assembler. It reconstructs long sequences of genomic DNA from fragmentary data produced by whole-genome shotgun sequencing