Awesome Bioinformatics

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

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.

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

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

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

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.

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

A fast and sensitive gapped read aligner

A Go package for engineering organisms.

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

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

Yet another redundant workflow engine

Efficient pythonic random access to fasta subsequences

JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.

Structural variant and indel caller for mapped sequencing data

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

cython + htslib == fast VCF and BCF processing

annotate a VCF with other VCFs/BEDs/tabixed files

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

Bayesian haplotype-based mutation calling

Core BioPerl 1.x code

Modular and universal bioinformatics

Reads simulator

Syntax highlighting for computational biology

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

Blazing-Fast Bioinformatic Operations on Python DataFrames

:rocket: seqfu - Sequece Fastx Utilities

Simple FASTQ quality assessment using Python

quickly filter fastq files by matching sequences to a set of regex patterns

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

This is the SeqWare Project's main repo.

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

Explore and analyze biological sequence data

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

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