Most popular bioinformatics repositories and open source projects

biofast

Benchmarking programming languages/implementations for common tasks in...

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smudgeplot

Inference of ploidy and heterozygosity structure using whole genome se...

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snpr

The sources of the openSNP website

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RaGOO

RaGOO is no longer supported. Please use RagTag instead: https://githu...

28   163   163  

cooler

A cool place to store your Hi-C

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diffxpy

Differential expression analysis for single-cell RNA-seq data.

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IMGTHLA

Github for files currently published in the IPD-IMGT/HLA FTP Directory...

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pegasus

Pegasus Workflow Management System - Automate, recover, and debug scie...

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readfq

Fast multi-line FASTA/Q reader in several programming languages

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shinyCircos

an R/shiny application for creation of Circos plot interactively

47   156   156  

sgas

SGAS: Sequential Greedy Architecture Search (CVPR'2020) https://www.de...

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p2rank

P2Rank: Protein-ligand binding site prediction tool based on machine l...

28   153   153  

redundans

Redundans is a pipeline that assists an assembly of heterozygous/polym...

20   153   153  

kmer-cnt

Code examples of fast and simple k-mer counters for tutorial purposes

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hts-nim

nim wrapper for htslib for parsing genomics data files

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sigminer

🌲 An easy-to-use and scalable toolkit for genomic alteration signatur...

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pyGenomeViz

A genome visualization python package for comparative genomics

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graphtyper

Population-scale genotyping using pangenome graphs

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jbrowse-components

Source code for JBrowse 2, a modern React-based genome browser

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TOBIAS

Transcription factor Occupancy prediction By Investigation of ATAC-seq...

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ngless

NGLess: NGS with less work

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cgranges

A C/C++ library for fast interval overlap queries (with a "bedtools co...

17   144   144  

indra

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an aut...

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GenomicSQLite

Genomics Extension for SQLite

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pymzML

pymzML - an interface between Python and mzML Mass spectrometry Files

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bioinformatics-workbook

Bioinformatics Workbook repository

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chromap

Fast alignment and preprocessing of chromatin profiles

17   141   141  

awesome-vdj

📚 Tools and databases for analyzing HLA and VDJ genes.

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biowasm

WebAssembly modules for genomics

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PyComplexHeatmap

PyComplexHeatmap: A Python package to plot complex heatmap (clustermap...

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ariba

Antimicrobial Resistance Identification By Assembly

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docker-builds

:package: :whale: Dockerfiles and documentation on tools for public he...

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InSilicoSeq

:rocket: A sequencing simulator

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MutScan

Detect and visualize target mutations by scanning FastQ files directly

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metaeuk

MetaEuk - sensitive, high-throughput gene discovery and annotation for...

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awesome-nanopore

A curated list of awesome nanopore analysis tools.

27   136   136  

YouTubeTutorials

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awesome-small-molecule-ml

A curated list of resources for machine learning for small-molecule dr...

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bio

Bioinformatics library for .NET

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svtools

Tools for processing and analyzing structural variants.

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MethylDackel

A (mostly) universal methylation extractor for BS-seq experiments.

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alphapept

A modular, python-based framework for mass spectrometry. Powered by nb...

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ComputationalGenomicsManual

Robs manual for the computational genomics and bioinformatics class.

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BioSequences.jl

Biological sequences for the julia language

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blasr

BLASR: The PacBio® long read aligner

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pydna

Clone with Python! Data structures for double stranded DNA & simulatio...

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psmc

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC...

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mag

Assembly and binning of metagenomes

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MSnbase

Base Classes and Functions for Mass Spectrometry and Proteomics

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rasusa

Randomly subsample sequencing reads to a specified coverage

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