Awesome Bioinformatics

:microscope: Path to a free self-taught education in Bioinformatics!

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

Official git repository for Biopython (originally converted from CVS)

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

A workflow language for data-driven computational pipelines

Single-cell analysis in Python. Scales to >100M cells.

A versatile pairwise aligner for genomic and spliced nucleotide sequences

MMseqs2: ultra fast and sensitive search and clustering suite

Useful bash one-liners for bioinformatics.

Tools (written in C using htslib) for manipulating next-generation sequencing data

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

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

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

Toolkit for processing sequences in FASTA/Q formats

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

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

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.

Accelerated BLAST compatible local sequence aligner.

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

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

RNAseq analysis notes from Ming Tang

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

Cloud-native genomic dataframes and batch computing

bedtools - the swiss army knife for genome arithmetic

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

:zap: :aquarius: Rapid prokaryotic genome annotation

SPAdes Genome Assembler

De novo assembler for single molecule sequencing reads using repeat graphs

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.

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

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

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

ChIP-seq analysis notes from Ming Tang

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

A fast and sensitive gapped read aligner

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

A Go package for engineering organisms.

A single molecule sequence assembler for genomes large and small.

C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

Create an index on a compressed text file

:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.

A quality control analysis tool for high throughput sequencing data

Yet another redundant workflow engine

Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/

Mummer alignment tool

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

SIFT

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

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