Package suites
- Bioconductor - A plethora of tools for analysis and comprehension of high-throughput genomic data, including 1500+ software packages. [ paper-2004 | web ]
- BioJulia - Bioinformatics and computational biology infastructure for the Julia programming language. [ web ]
Downloading
- GGD (⭐42) - Go Get Data; A command line interface for obtaining genomic data. [ web ]
Command Line Utilities
- BioNode (⭐313) - Modular and universal bioinformatics, Bionode provides pipeable UNIX command line tools and JavaScript APIs for bioinformatics analysis workflows. [ web ]
- bioSyntax (⭐271) - Syntax Highlighting for Computational Biology file formats (SAM, VCF, GTF, FASTA, PDB, etc...) in vim/less/gedit/sublime. [ paper-2018 | web ]
- csvtk (⭐1.2k) - Another cross-platform, efficient, practical and pretty CSV/TSV toolkit. [ web ]
- datamash - Data transformations and statistics. [ web ]
- easy_qsub (⭐29) - Easily submitting PBS jobs with script template. Multiple input files supported.
- GNU Parallel - General parallelizer that runs jobs in parallel on a single multi-core machine. Here are some example scripts using GNU Parallel. [ web ]
- grabix (⭐86) - A wee tool for random access into BGZF files.
- gsort (⭐36) - Sort genomic files according to a specified order.
Workflow Managers
- BigDataScript (⭐92) - A cross-system scripting language for working with big data pipelines in computer systems of different sizes and capabilities. [ paper-2014 | web ]
- Bpipe (⭐239) - A small language for defining pipeline stages and linking them together to make pipelines. [ web ]
- Common Workflow Language (⭐1.5k) - a specification for describing analysis workflows and tools that are portable and scalable across a variety of software and hardware environments, from workstations to cluster, cloud, and high performance computing (HPC) environments. [ web ]
- Galaxy - a popular open-source, web-based platform for data intensive biomedical research. Has several features, from data analysis to workflow management to visualization tools. [ paper-2018 | web ]
- Nextflow (⭐3.3k) (recommended) - A fluent DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner. [ paper-2018 | web ]
- Snakemake - A workflow management system in Python that aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment. [ paper-2018 | web ]
Pipelines
- bcbio-nextgen (⭐1k) - Batteries included genomic analysis pipeline for variant and RNA-Seq analysis, structural variant calling, annotation, and prediction. [ web ]
- R-Peridot (⭐7) - Customizable pipeline for differential expression analysis with an intuitive GUI. [ web ]
Sequence Processing
- FastQC (⭐591) - A quality control tool for high throughput sequence data. [ web ]
- Fastx Tookit (⭐199) - FASTQ/A short-reads pre-processing tools: Demultiplexing, trimming, clipping, quality filtering, and masking utilities. [ web ]
- Seqtk (⭐1.5k) - Toolkit for processing sequences in FASTA/Q formats.
Data Analysis
Sequence Alignment / Pairwise
- BWA (⭐1.7k) - Burrow-Wheeler Aligner for pairwise alignment between DNA sequences.
Variant Calling / Clustering
- GATK (⭐299) - Variant Discovery in High-Throughput Sequencing Data. [ web ]
Variant Calling / Structural variant callers
- smoove (⭐264) - structural variant calling and genotyping with existing tools, but,smoothly.
BAM File Utilities / Structural variant callers
- bam toolbox (⭐1) MtDNA:Nuclear Coverage; BAM Toolbox can output the ratio of MtDNA:nuclear coverage, a proxy for mitochondrial content.
- Telseq (⭐74) - Telseq is a tool for estimating telomere length from whole genome sequence data. [ paper-2014 ]
VCF File Utilities / Structural variant callers
- vcflib (⭐672) - A C++ library for parsing and manipulating VCF files.
GFF BED File Utilities / Structural variant callers
- BEDOPS - The fast, highly scalable and easily-parallelizable genome analysis toolkit. [ paper-2012 ]
Variant Simulation / Structural variant callers
- Bam Surgeon (⭐247) - Tools for adding mutations to existing
.bam files, used for testing mutation callers. [ web ]
Variant Prediction/Annotation / Structural variant callers
Python Modules / Data
Python Modules / Tools
Genome Browsers / Gene Diagrams / Tools
- Squiggle (⭐41) - Easy-to-use DNA sequence visualization tool that turns FASTA files into browser-based visualizations. [ paper-2018 | web ]
- biodalliance (⭐228) - Embeddable genome viewer. Integration data from a wide variety of sources, and can load data directly from popular genomics file formats including bigWig, BAM, and VCF.
[ paper-2011 | web ]
- BioJS (⭐507) - BioJS is a library of over hundred JavaScript components enabling you to visualize and process data using current web technologies. [ paper-2014 | web ]
- IGV js (⭐727) - Java-based browser. Fast, efficient, scalable visualization tool for genomics data and annotations. Handles a large variety of formats. [ paper-2019 | web ]
- PHAT (⭐17) - Point and click, cross platform suite for analysing and visualizing next-generation sequencing datasets. [ paper-2018 | web ]
- pileup.js (⭐280) - JavaScript library that can be used to generate interactive and highly customizable web-based genome browsers. [ paper-2016 ]
- Lucid Align - A modern sequence alignment viewer. [ web ]
Circos Related / Tools
- ClicO FS - An interactive web-based service of Circos. [ paper-2015 ]
- OmicCircos - R package for circular plots for omics data. [ paper-2014 | web ]
- J-Circos - A Java application for doing interactive work with circos plots. [ paper-2014 | web ]
Database Access / Tools
Becoming a Bioinformatician / Tools
- A Series of Interviews with Notable Bioinformaticians - Dr. Keith Bradnam "thought it might be instructive to ask a simple series of questions to a bunch of notable bioinformaticians to assess their feelings on the current state of bioinformatics research, and maybe get any tips they have about what has been useful to their bioinformatics careers."
- Rosalind - Rosalind is a platform for learning bioinformatics through problem solving.
Bioinformatics on GitHub / Tools
Sequencing / Tools
- For all you seq... (PDF) (3456x5471) - Massive infographic by Illumina on illustrating how many sequencing techniques work. Techniques cover protein-protein interactions, RNA transcription, RNA-protein interactions, RNA low-level detection, RNA modifications, RNA structure, DNA rearrangements and markers, DNA low-level detection, epigenetics, and DNA-protein interactions. References included.
RNA-Seq / Tools
- RNA-seqlopedia - RNA-seqlopedia provides an awesome overview of RNA-seq and of the choices necessary to carry out a successful RNA-seq experiment.
- Stories from the Supplement [46:39] - Dr. Lior Pachter shares his stories from the supplement for well-known RNA-seq analysis software CuffDiff and Cufflinks and explains some of their methodologies.
- List of RNA-seq Bioinformatics Tools - Extensive list on Wikipedia of RNA-seq bioinformatics tools needed in analysis, ranging from all parts of an analysis pipeline from quality control, alignment, splice analysis, and visualizations.
ChIP-Seq / Tools
YouTube Channels and Playlists / Tools
- Current Topics in Genome Analysis 2016 - Excellent series of fourteen lectures given at NIH about current topics in genomics ranging from sequence analysis, to sequencing technologies, and even more translational topics such as genomic medicine.
- GenomeTV - "GenomeTV is NHGRI's collection of official video resources from lectures, to news documentaries, to full video collections of meetings that tackle the research, issues and clinical applications of genomic research."
- NIH VideoCasting and Podcasting - "NIH VideoCast broadcasts seminars, conferences and meetings live to a world-wide audience over the Internet as a real-time streaming video." Not exclusively genomics and bioinformatics video but many great talks on domain specific use of bioinformatics and genomics.
Blogs / Tools
- ACGT - Dr. Keith Bradnam writes about this "thoughts on biology, genomics, and the ongoing threat to humanity from the bogus use of bioinformatics acroynums."
- Opiniomics - Dr. Mick Watson write on bioinformatics, genomes, and biology.
- Bits of DNA - Dr. Lior Pachter writes review and commentary on computational biology.
- it is NOT junk - Dr. Michael Eisen writes "a blog about genomes, DNA, evolution, open science, baseball and other important things"
Miscellaneous / Tools
- A New Online Computational Biology Curriculum - "This article introduces a catalog of several hundred free video courses of potential interest to those wishing to expand their knowledge of bioinformatics and computational biology. The courses are organized into eleven subject areas modeled on university departments and are accompanied by commentary and career advice."
Online networking groups / Tools
- COMBINE - An Austrialian group for bioinformatics students
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