Bioinformatics

Bioinformatics is an interdisciplinary field that intersects with biology, computer science, mathematics and statistics. It concerns itself with the development and use of methods and software tools for collecting and analyzing biological data.

GitHub: https://github.com/topics/bioinformatics
Wikipedia: https://en.wikipedia.org/wiki/Bioinformatics
Related Topics: genomics, sequencing,
Last updated: 2025-04-22 00:03:12 UTC
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https://github.com/Illumina/manta

Structural variant and indel caller for mapped sequencing data

bioinformatics indels structural-variation structural-variations

Last synced: 19 Apr 2025

https://github.com/openbiox/weekly

生信爱好者周刊（每周日发布）

bioinformatics free-journals weekly

Last synced: 13 Apr 2025

https://github.com/nf-core/sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

annotation bioinformatics cancer conda containers gatk4 genomics germline next-generation-sequencing nextflow nf-core pipeline pre-processing reproducible-research somatic target-panels variant-calling whole-exome-sequencing whole-genome-sequencing workflow

Last synced: 11 Apr 2025

https://github.com/FelixKrueger/Bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

bioinformatics dna methylation

Last synced: 30 Mar 2025

https://github.com/arvados/arvados

An open source platform for managing and analyzing biomedical big data

arvados aws azure bigdata bioinformatics cloud cluster cwl docker gcp genomics go python ruby workflow workflow-engine

Last synced: 14 Apr 2025

https://github.com/lh3/minigraph

Sequence-to-graph mapper and graph generator

bioinformatics genome-graph genomics pan-genome sequence-alignment

Last synced: 05 Apr 2025

https://github.com/haddocking/pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.

bioinformatics pdb protein python rcsb structural-bioinformatics structural-biology utrecht-university

Last synced: 22 Nov 2024

https://github.com/shenwei356/taxonkit

A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV

bioinformatics cross-platform lca lineage taxdump taxid taxonkit taxonomy

Last synced: 19 Apr 2025

https://github.com/fritzsedlazeck/survivor

Toolset for SV simulation, comparison and filtering

bioconda bioinformatics comparison simulator structural-variations survivor vcf

Last synced: 05 Apr 2025

https://github.com/Illumina/strelka

Strelka2 germline and somatic small variant caller

bioinformatics indels snps snvs

Last synced: 19 Apr 2025

https://github.com/mims-harvard/PrimeKG

Precision Medicine Knowledge Graph (PrimeKG)

bioinformatics dataset graph-machine-learning knowledge-graph network-medicine nlp-machine-learning precision-medicine therapeutics

Last synced: 13 Nov 2024

https://github.com/bioconvert/bioconvert

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

bam2cram bam2sam bcf2vcf bigbed2bed bioinformatics conversion convertor cram2bam cram2sam embl2ena embl2fasta embl2genbank fasta2fastq genbank2embl genbank2fasta ngs phylogeny sam2bam sequence sniffer

Last synced: 14 Nov 2024

https://github.com/brentp/vcfanno

annotate a VCF with other VCFs/BEDs/tabixed files

annotation bioinformatics genomics vcf

Last synced: 12 Apr 2025

https://github.com/brentp/cyvcf2

cython + htslib == fast VCF and BCF processing

bioinformatics cython genomics htslib vcf

Last synced: 11 Mar 2025

https://github.com/lh3/miniprot

Align proteins to genomes with splicing and frameshift

bioinformatics sequence-alignment

Last synced: 08 Apr 2025

https://github.com/alleninstitute/allensdk

code for reading and processing Allen Institute for Brain Science data

bioinformatics scientific

Last synced: 08 Apr 2025

https://github.com/theislab/cellrank

CellRank: dynamics from multi-view single-cell data

bioinformatics cell-fate-determination cell-fate-transitions data-science fuzzy-clustering-analyses genetics machine-learning manifold-learning markov-chains rna-velocity single-cell-genomics single-cell-rna-seq trajectory-generation

Last synced: 12 Nov 2024

https://github.com/illumina/strelka

Strelka2 germline and somatic small variant caller

bioinformatics indels snps snvs

Last synced: 05 Apr 2025

https://github.com/gao-lab/GLUE

Graph-linked unified embedding for single-cell multi-omics data integration

bioinformatics deep-learning single-cell single-cell-multiomics

Last synced: 23 Nov 2024

https://github.com/saketkc/pysradb

Package for fetching metadata and downloading data from SRA/ENA/GEO

bioinformatics bioinformatics-pipeline ena ncbi-sra ncbi-sra-archive sra sratoolkit

Last synced: 14 Apr 2025

https://github.com/sanger-pathogens/Roary

Rapid large-scale prokaryote pan genome analysis

bioinformatics bioinformatics-pipeline genomics global-health infectious-diseases next-generation-sequencing pathogen research sequencing

Last synced: 02 Apr 2025

https://github.com/bedops/bedops

:microscope: BEDOPS: high-performance genomic feature operations

bed bedops bioinformatics c c-plus-plus compression conversion genomics parallel pipeline set set-theory toolkit

Last synced: 04 Apr 2025

https://github.com/tariqdaouda/pygeno

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

bed bioinformatics biology cancer cancer-genomes cancer-genomics csv-parser ensembl genome genome-annotation genome-browser genome-sequencing genomes genomics gtf medical medicine proteomics snps vcf

Last synced: 04 Apr 2025

https://github.com/bcgsc/abyss

:microscope: Assemble large genomes using short reads

assembler bioinformatics bloom-filter c-plus-plus genome mpi openmp scaffold science

Last synced: 08 Apr 2025

https://github.com/bionode/bionode

Modular and universal bioinformatics

bioinformatics bionode metapackage nodejs os4openscience tools

Last synced: 05 Apr 2025

https://github.com/tariqdaouda/pyGeno

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

bed bioinformatics biology cancer cancer-genomes cancer-genomics csv-parser ensembl genome genome-annotation genome-browser genome-sequencing genomes genomics gtf medical medicine proteomics snps vcf

Last synced: 30 Mar 2025

https://github.com/lh3/miniasm

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

bioinformatics denovo-assembly genomics

Last synced: 12 Mar 2025

https://github.com/bioperl/bioperl-live

Core BioPerl 1.x code

bioinformatics bioperl perl toolkit

Last synced: 12 Apr 2025

https://github.com/brewsci/homebrew-bio

:beer::microscope: Bioinformatics formulae for the Homebrew package manager (macOS and Linux)

bioinformatics hacktoberfest homebrew linuxbrew science

Last synced: 29 Nov 2024

https://github.com/luntergroup/octopus

Bayesian haplotype-based mutation calling

bioinformatics de-novo-mutation genomics haplotypes phasing single-cell somatic-variants variant-calling variants

Last synced: 13 Nov 2024

https://github.com/bernatgel/karyoploteR

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

bioconductor bioinformatics data-visualization genome genomics-visualization plotting-in-r rstats

Last synced: 14 Nov 2024

https://github.com/neuhausi/canvasXpress

CanvasXpress: A JavaScript Library for Data Analytics with Full Audit Trail Capabilities.

analytics bioinformatics chart charting cran dash dashboard data-analytics data-science data-visualization genomics graphs javascript network network-visualization python r reproducible-research shiny visualization

Last synced: 04 Dec 2024

https://github.com/rvalieris/parallel-fastq-dump

parallel fastq-dump wrapper

bioinformatics

Last synced: 05 Apr 2025

https://github.com/wurmlab/sequenceserver

Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)

bioinformatics blast genomics genomics-visualization hacktoberfest javascript ruby sequence-alignment sequencing visualization

Last synced: 11 Apr 2025

https://github.com/mrolm/drep

Rapid comparison and dereplication of genomes

assembly bioinformatics metagenomics microbial-genomes microbiology

Last synced: 14 Apr 2025

https://github.com/marianattestad/ribbon

A genome browser designed for complex structural variants and long reads.

bioinformatics genome genomics visualization

Last synced: 12 Apr 2025

https://github.com/lmdu/pyfastx

a python package for fast random access to sequences from plain and gzipped FASTA/Q files

assembly bioinformatics biology dna fasta fastq genome python sequence

Last synced: 14 Apr 2025

https://github.com/moshi4/pygenomeviz

A genome visualization python package for comparative genomics

bioinformatics comparative-genomics genbank genomics genomics-visualization gff gff3 matplotlib microbial-genomics microbiology python synteny visualization

Last synced: 07 Apr 2025

https://github.com/lh3/wgsim

Reads simulator

bioinformatics genomics

Last synced: 09 Apr 2025

https://github.com/brentp/somalier

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

bioinformatics cancer-genomics genomics

Last synced: 11 Mar 2025

https://github.com/goekelab/bioinformatics-workflows

minimal example implementations for bioinformatics workflow managers

bioinformatics bioinformatics-workflows pipeline rna-seq workflow workflow-management

Last synced: 07 Apr 2025

https://github.com/WrightonLabCSU/DRAM

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

annotation bioinformatics genomics metagenome-assembled-genomes metagenomics microbiome viral-genomics viral-metagenomics

Last synced: 23 Mar 2025

https://github.com/ababaian/serratus

Ultra-deep search for novel viruses

aws bioinformatics coronavirus covid19 open-science sars-cov-2

Last synced: 07 Apr 2025

https://github.com/ncbi/amr

AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.

antibiotic-resistance bioinformatics genomics pathogen

Last synced: 23 Mar 2025

https://github.com/biosyntax/biosyntax

Syntax highlighting for computational biology

bam bioinformatics computational-biology fasta gedit less pdb sublime-text syntax-highlighting vcf vim

Last synced: 07 Apr 2025

https://gitlab.com/conradsnicta/armadillo-code

Armadillo: fast C++ library for linear algebra (matrix maths) & scientific computing - https://arma.sourceforge.net

BLAS C++ LAPACK Matrix-Factorization bioinformatics cpp high performance computing linear algebra linear-algebra-library machine learning matlab matrix inverse matrix-functions pattern recognition scientific computing signal processing statistics

Last synced: 12 Apr 2025

https://github.com/lynnlangit/gcp-for-bioinformatics

GCP for Bioinformatics Researchers

bioinformatics bioinformatics-analysis bioinformatics-pipeline bioinformatics-researchers gcp genomics google google-batch nextflow

Last synced: 12 Apr 2025

https://github.com/benlangmead/bowtie

An ultrafast memory-efficient short read aligner

bioinformatics c-plus-plus genomics read-aligners

Last synced: 06 Apr 2025

https://github.com/intermine/intermine

A powerful open source data warehouse system

api bioinformatics biology clojure clojurescript data-visualisation data-visualization data-warehouse genetics genomics java lgplv3 open-source opensource perl postgresql python tomcat tomcat8 webservices

Last synced: 08 Apr 2025

https://github.com/BenLangmead/bowtie

An ultrafast memory-efficient short read aligner

bioinformatics c-plus-plus genomics read-aligners

Last synced: 15 Mar 2025

https://github.com/bioSyntax/bioSyntax

Syntax highlighting for computational biology

bam bioinformatics computational-biology fasta gedit less pdb sublime-text syntax-highlighting vcf vim

Last synced: 13 Nov 2024

https://github.com/tiagoantao/bioinf-python

Python for Bioinformatics

bioinformatics python

Last synced: 09 Apr 2025

https://github.com/rdk/p2rank

P2Rank: Protein-ligand binding site prediction tool based on machine learning. Stand-alone command line program / Java library for predicting ligand binding pockets from protein structure.

binding-sites bioinformatics drug-discovery groovy java ligand machine-learning mmcif molecular-structures p2rank pdb protein-ligand-docking protein-ligand-interactions protein-structure protein-surface proteins pymol random-forest structural-bioinformatics virtual-screening

Last synced: 12 Apr 2025

https://github.com/linsalrob/computationalgenomicsmanual

Robs manual for the computational genomics and bioinformatics class.

bioinformatics genomics online-class

Last synced: 13 Apr 2025

https://github.com/nf-core/tools

Python package with helper tools for the nf-core community.

bioinformatics linter linting nextflow nf-core pipeline python workflow

Last synced: 09 Feb 2025

https://github.com/rcedgar/muscle

Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and predicted structures.

algorithms bioinformatics biology nucleotide-alignment protein-alignment protein-structure protein-structure-alignment sequence-clustering sequence-search

Last synced: 12 Apr 2025

https://github.com/nbisweden/mrbayes

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:

bayesian-inference bioinformatics markov-chain-monte-carlo phylogenetics research-tool

Last synced: 11 Apr 2025

https://github.com/KamilSJaron/smudgeplot

Inference of ploidy and heterozygosity structure using whole genome sequencing data

bioinformatics genomics kmer

Last synced: 28 Nov 2024

https://github.com/joergen7/cuneiform

Cuneiform distributed programming language

bioinformatics distributed-computing erlang functional-programming machine-learning otp parallelization workflow workflow-engine

Last synced: 12 Apr 2025

https://github.com/sanger-pathogens/snp-sites

Finds SNP sites from a multi-FASTA alignment file

bioinformatics bioinformatics-pipeline genomics global-health infectious-diseases next-generation-sequencing pathogen research sequencing

Last synced: 02 Apr 2025

https://github.com/deeptools/HiCExplorer

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

bioinformatics chromosome-conformation-capture galaxy genomics hic python

Last synced: 19 Apr 2025

https://github.com/edinburgh-genome-foundry/dnachisel

:pencil2: A versatile DNA sequence optimizer

bioinformatics codon-optimization dna-optimization sequence-design synbio synthetic-biology

Last synced: 13 Apr 2025

https://github.com/gmod/jbrowse-components

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

bioinformatics genomics jbrowse visualization

Last synced: 13 Apr 2025

https://github.com/aquaskyline/soapdenovo2

Next generation sequencing reads de novo assembler.

assembly bioinformatics computational-biology genome soapdenovo

Last synced: 06 Apr 2025

https://github.com/veg/hyphy

HyPhy: Hypothesis testing using Phylogenies

bioinformatics c-plus-plus comparative-genomics evolution phylogenetics science statistical-methods

Last synced: 08 Apr 2025

https://github.com/Benjamin-Lee/deep-rules

Ten Quick Tips for Deep Learning in Biology

bioinformatics biology computational-biology data-science deep-learning genomics machine-learning manubot manuscript

Last synced: 12 Nov 2024

https://github.com/mbhall88/rasusa

Randomly subsample sequencing reads or alignments

alignment bam bioinformatics coverage downsample fasta fastq genome-analysis random rust subsampling

Last synced: 07 Apr 2025

https://github.com/sortmerna/sortmerna

SortMeRNA: next-generation sequence filtering and alignment tool

alignment bioinformatics cpp metatranscriptomics ngs python sequencing

Last synced: 06 Apr 2025

https://github.com/althonos/pronto

A Python frontend to (Open Biomedical) Ontologies.

bioinformatics obo obo-graphs obofoundry ontology owl parser python semantic-web

Last synced: 12 Apr 2025

https://github.com/biocypher/biocypher

A unifying framework for biomedical research knowledge graphs

ai-ready biochatter bioinformatics biomedical framework knowledge-graph neo4j ontology postgresql rdf rdfs retrieval-augmented-generation sql

Last synced: 07 Apr 2025

https://github.com/brentp/goleft

goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary

bioinformatics coverage depth genomics golang

Last synced: 09 Apr 2025

https://linsalrob.github.io/ComputationalGenomicsManual/

Robs manual for the computational genomics and bioinformatics class.

bioinformatics genomics online-class

Last synced: 13 Nov 2024

https://github.com/biowasm/biowasm

WebAssembly modules for genomics

awk bedtools bioinformatics bowtie2 genomics grep javascript jq minimap2 samtools sed seqtk webassembly

Last synced: 12 Apr 2025

https://github.com/fbreitwieser/krakenuniq

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results

bioinformatics metagenomics

Last synced: 13 Nov 2024

https://github.com/slowkow/harmonypy

🎼 Integrate multiple high-dimensional datasets with fuzzy k-means and locally linear adjustments.

bioinformatics data-integration data-science single-cell-analysis

Last synced: 04 Apr 2025

https://github.com/ugeneunipro/ugene

UGENE is free open-source cross-platform bioinformatics software

bioinformatics cpp cross-platform dna msa ngs pipeline qt5 science sequencing ugene workflow

Last synced: 03 Apr 2025

https://github.com/opengene/afterqc

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

adapter-trimming bioinformatics error fastq filtering ngs overlap qc quality-control sequencing trimming

Last synced: 17 Mar 2025

https://github.com/OpenGene/AfterQC

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

adapter-trimming bioinformatics error fastq filtering ngs overlap qc quality-control sequencing trimming

Last synced: 13 Nov 2024

https://github.com/lh3/gfatools

Tools for manipulating sequence graphs in the GFA and rGFA formats

bioinformatics genome-graph genomics

Last synced: 26 Feb 2025

https://github.com/privefl/bigsnpr

R package for the analysis of massive SNP arrays.

big-data bioinformatics memory-mapped-file parallel-computing polygenic-scores population-structure-inference r r-package snp-data statistical-methods

Last synced: 04 Dec 2024

https://github.com/lazear/sage

Proteomics search & quantification so fast that it feels like magic

bioinformatics mass-spectrometry proteomics

Last synced: 12 Nov 2024

https://github.com/widdowquinn/pyani

Application and Python module for average nucleotide identity analyses of microbes.

ani average-nucleotide-identity bioinformatics classification taxonomy taxonomy-assignment

Last synced: 07 Apr 2025

https://github.com/haowenz/chromap

Fast alignment and preprocessing of chromatin profiles

bioinformatics chromatin-profiles genomics sequence-analysis

Last synced: 16 Nov 2024

https://github.com/pegasus-isi/pegasus

Pegasus Workflow Management System - Automate, recover, and debug scientific computations.

bioinformatics distributed-systems hpc workflow workflow-management-system

Last synced: 06 Apr 2025

https://github.com/mikelove/bioc-refcard

Bioconductor cheat sheet

bioconductor bioinformatics cheatsheet compbio guide howto microarray r rnaseq

Last synced: 10 Jan 2025

https://github.com/broadinstitute/gatk-sv

A structural variation pipeline for short-read sequencing

bioinformatics genomics structural-variants structural-variation

Last synced: 12 Apr 2025

https://github.com/sorgerlab/indra

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

bioinformatics biology computational-biology indra modeling nlp pysb sbml systems-biology

Last synced: 15 Apr 2025

https://github.com/saezlab/decoupler-py

Python package to perform enrichment analysis from omics data.

bioinformatics data-science enrichment enrichment-analysis numba python single-cell spatial-transcriptomics transcriptomics

Last synced: 10 Apr 2025

https://github.com/salvatorera/tutorial

Tutorials on machine learning, artificial intelligence, data science with math explanation and reusable code (in python and R)

artificial-intelligence bioinformatics biology computer-vision convolutional-neural-networks data-science deep-learning graph image machine-learning natural-language-processing nlp python r streamlit streamlit-webapp tutorial tutorials vision-transformer

Last synced: 04 Apr 2025

https://github.com/open2c/bioframe

Genomic interval operations on Pandas DataFrames

bioinformatics dataframes genomic-intervals genomic-ranges genomics ngs-analysis numpy pandas python spatial-join

Last synced: 07 Apr 2025

https://github.com/soedinglab/metaeuk

MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics

bioinformatics eukaryotes gene-discovery gene-prediction metagenomics

Last synced: 17 Mar 2025

https://github.com/typedb/biograkn

BioGrakn Knowledge Graph

biograkn bioinformatics biomedical knowledge-discovery knowledge-graph

Last synced: 03 Apr 2025

https://github.com/lh3/biofast

Benchmarking programming languages/implementations for common tasks in Bioinformatics

bioinformatics

Last synced: 17 Nov 2024

https://github.com/lh3/pangene

Constructing a pangenome gene graph

bioinformatics pangenome

Last synced: 10 Feb 2025

https://github.com/franciscozorrilla/metaGEM

:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

bioinformatics computational-biology flux-balance-analysis genome-scale-metabolic-model gut-microbiome mags metabolic-modeling metabolic-models metabolism metagenome-assembled-genomes metagenomics microbial-ecology microbiome snakemake systems-biology