Most popular bioinformatics repositories and open source projects

bcalm

compacted de Bruijn graph construction in low memory

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assembly-stats

Get assembly statistics from FASTA and FASTQ files

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python_biologist

Python Programming for Biologists

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owltools

OWLTools

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HoneyBADGER

HMM-integrated Bayesian approach for detecting CNV and LOH events from...

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reg-gen

Regulatory Genomics Toolbox: Python library and set of tools for the i...

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run_dbcan

Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled org...

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CAFE

Analyze changes in gene family size and provide a statistical foundati...

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awesome-genetics

A curated list of awesome bioinformatics software.

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BWA-MEME

BWA-MEME: Faster BWA-MEM2 using learned-index

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bio_scripts

Practical, reusable scripts for bioinformatics

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What_the_Phage

WtP: Phage identification via nextflow and docker or singularity

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yak

Yet another k-mer analyzer

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af2complex

Predicting direct protein-protein interactions with AlphaFold deep lea...

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gramtools

Genome inference from a population reference graph

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open-cravat

A modular annotation tool for genomic variants

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smk-simple-slurm

A simple Snakemake profile for Slurm without --cluster-config

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RIDDLE

Race and ethnicity Imputation from Disease history with Deep LEarning

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biomake

GNU-Make-like utility for managing builds and complex workflows

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freesasa

C-library for calculating Solvent Accessible Surface Areas

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bgt

Flexible genotype query among 30,000+ samples whole-genome

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goenrich

GO enrichment with python -- pandas meets networkx

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havengrc

☁️Haven GRC - easier governance, risk, and compliance 👨‍⚕️👮‍♀️🦸‍♀️🕵️‍♀...

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UCSCXenaTools

:package: An R package for accessing genomics data from UCSC Xena plat...

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rBLAST

Interface for the Basic Local Alignment Search Tool (BLAST) - R-Packag...

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cljam

A DNA Sequence Alignment/Map (SAM) library for Clojure

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platon

Identification & characterization of bacterial plasmid-borne contigs f...

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foldcomp

Compressing protein structures effectively with torsion angles

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CharGer

Characterization of Germline variants

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arcs

🌈Scaffold genome sequence assemblies using linked or long read sequenc...

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snakefiles

:snake: Snakefiles for common RNA-seq data analysis workflows (STAR an...

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referenceseeker

Rapid determination of appropriate reference genomes.

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QUBEKit

Quantum Mechanical Bespoke Force Field Derivation Toolkit

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TOGA

TOGA (Tool to infer Orthologs from Genome Alignments): implements a no...

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wgdi

WGDI: A user-friendly toolkit for evolutionary analyses of whole-genom...

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decoupler-py

Python package to infer biological activities from omics data using a...

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hickit

TAD calling, phase imputation, 3D modeling and more for diploid single...

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minced

Mining CRISPRs in Environmental Datasets

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PyWGCNA

PyWGCNA is a Python package designed to do Weighted Gene Correlation N...

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awesome-10x-genomics

List of tools and resources related to the 10x Genomics GEMCode/Chromi...

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bget

Portable command-line tool to query bioinformatics APIs, data, databas...

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flo

Same species annotation lift over pipeline.

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PyFeat

A Python-based Effective Feature Generation Tool from DNA, RNA, and Pr...

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skani

Fast, robust ANI and aligned fraction for metagenomic genomes and cont...

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STARTapp

The START App: R Shiny Transcriptome Analysis Resource Tool

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dammit

just annotate it, dammit!

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flowr

Robust and efficient workflows using a simple language agnostic approa...

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myvariant.info

MyVariant.info: A BioThings API for human variant annotations

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bio

A lightweight and high-performance bioinformatics package in Golang

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dgenies

Dotplot large Genomes in an Interactive, Efficient and Simple way

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