Awesome Bioinformatics

A flexible pipeline for complete analysis of bacterial genomes

The Leek group guide to genomics papers

🔬A library of JavaScript components to represent biological data

Efficient pythonic random access to fasta subsequences

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

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

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

A Variant Call Format reader for Python.

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

annotate a VCF with other VCFs/BEDs/tabixed files

Access to Biological Web Services from Python.

lumpy: a general probabilistic framework for structural variant discovery

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

Python wrapper -- and more -- for BEDTools (bioinformatics tools for "genome arithmetic")

Bayesian haplotype-based mutation calling

No description.

Core BioPerl 1.x code

GFF and GTF file manipulation and interconversion

Modular and universal bioinformatics

Genomic variant annotation and functional effect prediction

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

Reads simulator

Pairwise Sequence Alignment Library

GRIDSS: the Genomic Rearrangement IDentification Software Suite

Interactive in-browser track viewer

Syntax highlighting for computational biology

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

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

Bpipe - a tool for running and managing bioinformatics pipelines

WFA-lib: Wavefront alignment algorithm library v2

Interactive web-based genome browser.

Web application to explore the Sequence Read Archive.

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

Blazing-Fast Bioinformatic Operations on Python DataFrames

FASTA/FASTQ pre-processing programs

A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF, 23andMe...), up to 5x better than gzip and faster too

Scalable gVCF merging and joint variant calling for population sequencing projects

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

A powerful toolset for genome arithmetic.

python access to UCSC genomes database

:rocket: seqfu - Sequece Fastx Utilities

SKESA assembler

OCaml Bioinformatics Library

An imagemagick-like frontend to Biopython SeqIO

Simple FASTQ quality assessment using Python

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

:mount_fuji: Fuji plot—a circos representation of multiple GWAS results— :mount_fuji: