Awesome Bioinformatics

Core BioPerl 1.x code

Official git repository for Biopython (originally converted from CVS)

This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

A Go package for engineering organisms.

OCaml Bioinformatics Library

The command-line interface to GGD

Web application to explore the Sequence Read Archive.

Compressor for genomic files (FASTQ, SAM/BAM, VCF, FASTA, GVF, 23andMe...), up to 5x better than gzip and faster too

Useful bash one-liners for bioinformatics.

Modular and universal bioinformatics

Syntax highlighting for computational biology

A suite of utilities for converting to and working with CSV, the king of tabular file formats.

A cross-platform, efficient and practical CSV/TSV toolkit in Golang

Easily submitting multiple PBS jobs or running local jobs in parallel. Multiple input files supported.

a wee tool for random access into BGZF files.

sort genomic data

Note: tabix and bgzip binaries are now part of the HTSlib project.

Write-once-read-many table for large datasets.

Create an index on a compressed text file

BigDataScript: Scirpting language for big data

Bpipe - a tool for running and managing bioinformatics pipelines

Repository for the CWL standards. Use https://cwl.discourse.group/ for support 😊

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

A DSL for data-driven computational pipelines

Yet another redundant workflow engine

CGAT-ruffus is a lightweight python module for running computational pipelines

Robust, flexible and resource-efficient pipelines using Go and the commandline

This is the SeqWare Project's main repo.

Workflow Description Language - Specification and Implementations

A curated list of awesome pipeline toolkits inspired by Awesome Sysadmin

A flexible pipeline for complete analysis of bacterial genomes

Generic but comprehensive pipeline for prokaryotic genome annotation and interrogation with interactive reports and shiny app.

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

Software for intuitively doing Differential Gene Expression (DGE) analysis on Windows and GNU\Linux, based on R packages.

A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

A quality control analysis tool for high throughput sequencing data

Simple FASTQ quality assessment using Python

FASTA/FASTQ pre-processing programs

Aggregate results from bioinformatics analyses across many samples into a single report.

seqfu - Sequece Fastx Utilities

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang

An imagemagick-like frontend to Biopython SeqIO

Toolkit for processing sequences in FASTA/Q formats

Explore and analyze biological sequence data

Scalable genomic data analysis.

Scalable gVCF merging and joint variant calling for population sequencing projects

A fast and sensitive gapped read aligner

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

Wavefront alignment algorithm (WFA): Fast and exact gap-affine pairwise alignment

Pairwise Sequence Alignment Library

Mummer alignment tool

Accelerated BLAST compatible local sequence aligner.

A simple Partial Order Aligner based on Lee, Grasso and Sharlow (2002), for education/demonstration purposes

MMseqs2: ultra fast and sensitive search and clustering suite

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

Official code repository for GATK versions 1.0 through 3.7 (core engine). For GATK 4 code, see the https://github.com/broadinstitute/gatk repository

Bayesian haplotype-based mutation calling

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

lumpy: a general probabilistic framework for structural variant discovery

Structural variant and indel caller for mapped sequencing data

GRIDSS: the Genomic Rearrangement IDentification Software Suite

structural variant calling and genotyping with existing tools, but, smoothly.

C++ API & command-line toolkit for working with BAM data

A bam toolbox

Automate common sam & bam conversions

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

SAMStat displays various properties of next-generation sequencing reads stored in SAM/BAM format.

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"

A software for calculating telomere length

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html

annotate a VCF with other VCFs/BEDs/tabixed files

C++ library and cmdline tools for parsing and manipulating VCF files

A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.

Another Gtf/Gff Analysis Toolkit

GFF and GTF file manipulation and interconversion

bedtools - the swiss army knife for genome arithmetic

tools for adding mutations to existing .bam files, used for testing mutation callers

Reads simulator

SIFT

python access to UCSC genomes database

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl

Access to Biological Web Services from Python.

A fast Python library for VCF files leveraging Cython for speed.

cython + htslib == fast VCF and BCF processing

Python wrapper -- and more -- for Aaron Quinlan's BEDTools (bioinformatics tools)

Efficient pythonic random access to fasta subsequences

Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib C-API, the same one that powers samtools, bcftools, and tabix.

A Variant Call Format reader for Python.

SPAdes Genome Assembler

SKESA assembler

Rapid prokaryotic genome annotation

Rapid & standardized annotation of bacterial genomes & plasmids

A single molecule sequence assembler for genomes large and small.

De novo assembler for single molecule sequencing reads using repeat graphs

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

Redbean: A fuzzy Bruijn graph approach to long noisy reads assembly

📈 DNA Sequence Visualization for Humans

Interactive web-based genome browser.

🔬A library of JavaScript components to represent biological data

Flexible circular visualization of genome-associated data with BioPerl and SVG.

Horizon chart js library for DNA data.

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

SVG based genome viewer written in javascript using D3

A modern genome browser built with JavaScript and HTML5.

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

Interactive in-browser track viewer

HTML5 canvas genomic graphics library

Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationships between objects or positions.

Fuji plot—a circos representation of multiple GWAS results—

Path to a free self-taught education in Bioinformatics!

Alternative splicing resource

A collection of research papers for AI-based protein design

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

RNAseq analysis notes from Ming Tang

ChIP-seq analysis notes from Ming Tang

The Leek group guide to genomics papers