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: 2026-03-22 00:03:31 UTC
- JSON Representation
https://github.com/developer-y/cs-video-courses
List of Computer Science courses with video lectures.
algorithms bioinformatics computational-biology computational-physics computer-architecture computer-science computer-vision database-systems databases deep-learning embedded-systems machine-learning quantum-computing reinforcement-learning robotics security systems web-development
Last synced: 30 Jul 2025
https://github.com/Developer-Y/cs-video-courses
List of Computer Science courses with video lectures.
algorithms bioinformatics computational-biology computational-physics computer-architecture computer-science computer-vision database-systems databases deep-learning embedded-systems machine-learning quantum-computing reinforcement-learning robotics security systems web-development
Last synced: 13 Mar 2025
https://github.com/plotly/dash
Data Apps & Dashboards for Python. No JavaScript Required.
bioinformatics charting dash data-science data-visualization finance flask gui-framework jupyter modeling plotly plotly-dash productivity python react rstats technical-computing web-app
Last synced: 12 May 2025
https://github.com/biopython/biopython
Official git repository for Biopython (originally converted from CVS)
bioinformatics biopython dna genomics phylogenetics protein protein-structure python sequence-alignment
Last synced: 13 May 2025
https://github.com/google/deepvariant
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
bioinformatics deep-learning deep-neural-network deepvariant dna genome genomics machine-learning ngs science sequencing tensorflow
Last synced: 13 May 2025
https://github.com/nextflow-io/nextflow
A DSL for data-driven computational pipelines
aws bioinformatics cloud dataflow docker groovy hello hpc nextflow pipeline pipeline-framework reproducible-research reproducible-science sge singularity singularity-containers slurm workflow-engine
Last synced: 13 May 2025
https://github.com/sokrypton/colabfold
Making Protein folding accessible to all!
bioinformatics multiple-sequence-alignment protein-structure structure-prediction
Last synced: 07 Mar 2026
https://github.com/scverse/scanpy
Single-cell analysis in Python. Scales to >100M cells.
anndata bioinformatics data-science machine-learning python scanpy scverse transcriptomics visualize-data
Last synced: 11 May 2025
https://github.com/opengene/fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
adapter bioinformatics duplication fastq filter filtering illumina merging ngs overlap polyg preprocessing qc quality quality-control sequencing splitting trimming umi
Last synced: 23 Jan 2026
https://github.com/OpenGene/fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
adapter bioinformatics duplication fastq filter filtering illumina merging ngs overlap polyg preprocessing qc quality quality-control sequencing splitting trimming umi
Last synced: 07 May 2025
https://github.com/sokrypton/ColabFold
Making Protein folding accessible to all!
bioinformatics multiple-sequence-alignment protein-structure structure-prediction
Last synced: 27 Mar 2025
https://github.com/lh3/minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences
bioinformatics genomics sequence-alignment spliced-alignment
Last synced: 23 Apr 2025
https://github.com/broadinstitute/gatk
Official code repository for GATK versions 4 and up
bioinformatics dna gatk genome genomics ngs science sequencing spark
Last synced: 14 May 2025
https://github.com/allenai/scispacy
A full spaCy pipeline and models for scientific/biomedical documents.
bioinformatics biomedical custom-pipes nlp scientific-documents spacy
Last synced: 13 May 2025
https://github.com/bioconda/bioconda-recipes
Conda recipes for the bioconda channel.
bioinformatics conda hacktoberfest package-management
Last synced: 14 May 2025
https://allenai.github.io/scispacy/
A full spaCy pipeline and models for scientific/biomedical documents.
bioinformatics biomedical custom-pipes nlp scientific-documents spacy
Last synced: 10 Jul 2025
https://github.com/soedinglab/mmseqs2
MMseqs2: ultra fast and sensitive search and clustering suite
alignment bioinformatics blast linclust metagenomics mmseqs profile-search sequence-clustering sequence-search taxonomy
Last synced: 05 Oct 2025
https://github.com/lh3/bwa
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
bioinformatics fm-index genomics sequence-alignment
Last synced: 10 Apr 2025
https://github.com/galaxyproject/galaxy
Data intensive science for everyone.
bioinformatics dna genomics hacktoberfest ngs pipeline science sequencing usegalaxy workflow workflow-engine
Last synced: 11 May 2025
https://github.com/lh3/seqtk
Toolkit for processing sequences in FASTA/Q formats
bioinformatics sequence-analysis
Last synced: 15 May 2025
https://github.com/soedinglab/MMseqs2
MMseqs2: ultra fast and sensitive search and clustering suite
alignment bioinformatics blast linclust metagenomics mmseqs profile-search sequence-clustering sequence-search taxonomy
Last synced: 05 May 2025
https://github.com/crazyhottommy/getting-started-with-genomics-tools-and-resources
Unix, R and python tools for genomics and data science
bioinformatics cancer-genomics data-science
Last synced: 06 Oct 2025
https://github.com/shenwei356/seqkit
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
bioinformatics cross-platform fasta fastq golang manipulation sequence tool toolkit
Last synced: 29 Dec 2025
https://github.com/multiqc/multiqc
Aggregate results from bioinformatics analyses across many samples into a single report.
analysis bioconda bioinformatics data-visualization multiqc pypi python quality-control reporting seqera vizualisation
Last synced: 04 Mar 2026
https://github.com/MultiQC/MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
analysis bioconda bioinformatics data-visualization multiqc pypi python quality-control reporting seqera vizualisation
Last synced: 05 May 2025
https://github.com/lightaime/deep_gcns_torch
Pytorch Repo for DeepGCNs (ICCV'2019 Oral, TPAMI'2021), DeeperGCN (arXiv'2020) and GNN1000(ICML'2021): https://www.deepgcns.org
3d-point-clouds bioinformatics cheminformatics computer-vision data-mining deep-gcns deep-learning geometric-deep-learning graph-convolutional-networks graph-neural-networks pytorch science-research social-network
Last synced: 16 May 2025
https://github.com/scikit-bio/scikit-bio
scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.
bioinformatics computational-biology
Last synced: 21 Feb 2026
https://github.com/scipipe/scipipe
Robust, flexible and resource-efficient pipelines using Go and the commandline
bioinformatics bioinformatics-pipeline cheminformatics dataflow fbp go golang pipeline scientific-workflows scipipe workflow workflow-engine
Last synced: 15 Dec 2025
https://github.com/a-r-j/graphein
Protein Graph Library
bioinformatics computational-biology deep-learning dgl drug-discovery gene-regulatory-networks geometric-deep-learning graph-neural-networks interactome interactomics ppi-networks protein protein-data-bank protein-design protein-structure python pytorch pytorch-geometric rna structural-biology
Last synced: 14 May 2025
https://github.com/shenwei356/rush
A cross-platform command-line tool for executing jobs in parallel
bioinformatics command cross-platform execute golang parallel pipeline shell windows
Last synced: 16 Jan 2026
https://github.com/shenwei356/csvtk
A cross-platform, efficient and practical CSV/TSV toolkit in Golang
bioinformatics command-line cross-platform csv golang tool toolkit tsv
Last synced: 29 Dec 2025
https://github.com/kblin/ncbi-genome-download
Scripts to download genomes from the NCBI FTP servers
bioinformatics biology command-line download-genomes genbank genomics ncbi python
Last synced: 17 Jan 2026
https://github.com/plotly/react-plotly.js
A plotly.js React component from Plotly 📈
bioinformatics charting-library d3 data-visualization fintech plotly react
Last synced: 13 May 2025
https://github.com/steineggerlab/foldseek
Foldseek enables fast and sensitive comparisons of large structure sets.
alignments bioinformatics clustering protein-structure
Last synced: 05 Oct 2025
https://github.com/kexinhuang12345/deeppurpose
A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)
bioinformatics covid19 ddi deep-learning drug-discovery drug-drug-interaction drug-property-prediction drug-repurposing drug-target-interaction drug-target-interactions dti-prediction ppi protein-function-prediction protein-protein-interaction qsar repurposing-drugs side-effects toolkit virtual-screening
Last synced: 02 Jul 2025
https://github.com/mims-harvard/TDC
Therapeutics Commons (TDC-2): Multimodal Foundation for Therapeutic Science
artificial-intelligence benchmarks bioinformatics biology biomedicine biotech cheminformatics chemistry datasets deep-learning drug-discovery machine-learning medicine precision-medicine therapeutics
Last synced: 30 Mar 2025
https://github.com/kexinhuang12345/DeepPurpose
A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)
bioinformatics covid19 ddi deep-learning drug-discovery drug-drug-interaction drug-property-prediction drug-repurposing drug-target-interaction drug-target-interactions dti-prediction ppi protein-function-prediction protein-protein-interaction qsar repurposing-drugs side-effects toolkit virtual-screening
Last synced: 03 Apr 2025
https://github.com/hail-is/hail
Cloud-native genomic dataframes and batch computing
bioinformatics genetics genomics gwas hail python software vcf
Last synced: 13 May 2025
https://github.com/moshi4/pyCirclize
Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)
bioinformatics chord-diagram circos comparative-genomics data-visualization dataviz genomics genomics-visualization matplotlib microbial-genomics phylogenetic-trees python radar-chart visualization
Last synced: 18 Nov 2025
https://github.com/broadinstitute/cromwell
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
application bioinformatics cloud containers docker executor ga4gh hpc scala wdl workflow workflow-description-language workflow-execution
Last synced: 27 Mar 2025
https://github.com/biocore/scikit-bio
scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.
bioinformatics computational-biology
Last synced: 17 Aug 2025
https://github.com/biotite-dev/biotite
A comprehensive library for computational molecular biology
bioinformatics computational-biology pdb-files sequence-analysis structural-biology
Last synced: 22 Jan 2026
https://github.com/pysam-developers/pysam
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.
bioinformatics htslib ngs python
Last synced: 18 Feb 2026
https://github.com/moshi4/pycirclize
Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)
bioinformatics chord-diagram circos comparative-genomics data-visualization dataviz genomics genomics-visualization matplotlib microbial-genomics phylogenetic-trees python radar-chart visualization
Last synced: 14 May 2025
https://github.com/samtools/htslib
C library for high-throughput sequencing data formats
bam bcf bioinformatics cram htslib ngs sam vcf
Last synced: 29 Dec 2025
https://github.com/openwdl/wdl
Specification for the Workflow Description Language (WDL).
bioinformatics cloud openwdl reproducibility reproducible-science wdl workflow
Last synced: 15 Feb 2026
https://github.com/baranzinilab/kg_rag
Empower Large Language Models (LLM) using Knowledge Graph based Retrieval-Augmented Generation (KG-RAG) for knowledge intensive tasks
bert-models bioinformatics bioinformatics-algorithms biomedical-applications biomedical-informatics context-aware gpt gpt35turbo gpt4 knowledge-base knowledge-graph large-language-models llama llama2 llm prompt-engineering prompt-tuning rag retrieval-augmented-generation sentence-transformers
Last synced: 04 Oct 2025
https://github.com/tanghaibao/jcvi
Python library to facilitate genome assembly, annotation, and comparative genomics
allmaps assembly bioinformatics blast comparative-genomics genetic-maps genome-sequencing genomics sequence-alignments synteny variant-calling
Last synced: 14 May 2025
https://github.com/google/nucleus
Python and C++ code for reading and writing genomics data.
bioinformatics dna genomics tensorflow
Last synced: 30 Sep 2025
https://github.com/dib-lab/khmer
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
bioinformatics bloom-filter count-min-sketch dna graph-traversal k-mer python
Last synced: 19 Jan 2026
https://github.com/danforthcenter/plantcv
Plant phenotyping with image analysis
bioinformatics image-analysis plant-phenotyping plantcv science
Last synced: 28 Jan 2026
https://github.com/awslabs/dgl-lifesci
Python package for graph neural networks in chemistry and biology
bioinformatics cheminformatics deep-learning dgl drug-discovery geometric-deep-learning graph-neural-networks molecule
Last synced: 15 May 2025
https://github.com/COMBINE-lab/salmon
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
10x bioinformatics c-plus-plus gene-expression quantification quasi-mapping rna-seq rna-seq-quantification rnaseq sailfish salmon scrna-seq selective-alignment single-cell single-cell-rna-seq transcriptome
Last synced: 11 May 2025
https://github.com/bebop/poly
A Go package for engineering organisms.
alignment bioengineering bioinformatics codon-optimizer computational-biology dna dna-barcode dna-barcoding fasta genbank genetic-engineering go golden-gate mash molecular-biology plasmids primer-design sequence-hashing synbio synthetic-biology
Last synced: 11 Mar 2026
https://github.com/biocontainers/containers
Bioinformatics containers
biocontainers-architecture bioinformatics bioinformatics-analysis bioinformatics-containers docker-image dockerfiles rkt
Last synced: 14 May 2025
https://github.com/torognes/vsearch
Versatile open-source tool for microbiome analysis
amplicon bioinformatics chimera clustering fasta fastq metabarcoding metagenomics microbiome search sequence-alignment
Last synced: 21 Oct 2025
https://github.com/deeptools/deepTools
Tools to process and analyze deep sequencing data.
bioinformatics chip-seq genomics ngs python rna-seq
Last synced: 19 Apr 2025
https://github.com/benlangmead/bowtie2
A fast and sensitive gapped read aligner
bioinformatics c-plus-plus genomics read-aligners
Last synced: 15 May 2025
https://github.com/biopandas/biopandas
Working with molecular structures in pandas DataFrames
bioinformatics computational-biology drug-discovery mol2 molecular-structures molecule molecules pandas-dataframe pdb pdb-files protein-structure
Last synced: 16 May 2025
https://github.com/BioPandas/biopandas
Working with molecular structures in pandas DataFrames
bioinformatics computational-biology drug-discovery mol2 molecular-structures molecule molecules pandas-dataframe pdb pdb-files protein-structure
Last synced: 18 Jul 2025
https://rasbt.github.io/biopandas
Working with molecular structures in pandas DataFrames
bioinformatics computational-biology drug-discovery mol2 molecular-structures molecule molecules pandas-dataframe pdb pdb-files protein-structure
Last synced: 05 Sep 2025
https://github.com/BioContainers/containers
Bioinformatics containers
biocontainers-architecture bioinformatics bioinformatics-analysis bioinformatics-containers docker-image dockerfiles rkt
Last synced: 04 May 2025
https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer
:eye: Python library to plot DNA sequence features (e.g. from Genbank files)
bioinformatics dna-visualization genbank molecular-biology synthetic-biology visualization
Last synced: 23 Nov 2025
https://github.com/BaranziniLab/KG_RAG
Empower Large Language Models (LLM) using Knowledge Graph based Retrieval-Augmented Generation (KG-RAG) for knowledge intensive tasks
bert-models bioinformatics bioinformatics-algorithms biomedical-applications biomedical-informatics context-aware gpt gpt35turbo gpt4 knowledge-base knowledge-graph large-language-models llama llama2 llm prompt-engineering prompt-tuning rag retrieval-augmented-generation sentence-transformers
Last synced: 24 Mar 2025
https://github.com/BenLangmead/bowtie2
A fast and sensitive gapped read aligner
bioinformatics c-plus-plus genomics read-aligners
Last synced: 05 May 2025
https://github.com/owkin/PyDESeq2
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
bioinformatics differential-expression python rna-seq transcriptomics
Last synced: 09 May 2025
https://github.com/voutcn/megahit
Ultra-fast and memory-efficient (meta-)genome assembler
bioinformatics data-structures genome-assembly genomics metagenomics succinct
Last synced: 21 Oct 2025
https://github.com/pharmai/plip
Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Schake, Bolz, et al. (2025), https://doi.org/10.1093/nar/gkaf361
bioinformatics docker openbabel pdb plip protein-structure python-bindings scientific-computing singularity
Last synced: 18 Feb 2026
https://github.com/scverse/anndata
Annotated data.
anndata bioinformatics data-science machine-learning scanpy scverse transcriptomics
Last synced: 29 Jan 2026
https://github.com/cafferychen777/mllmcelltype
Cell type annotation for single-cell RNA-seq using multi-LLM consensus
bioinformatics cell-type-annotation computational-biology consensus-algorithm large-language-models llm scanpy scrna scrnaseq-analysis seurat single-cell
Last synced: 08 Feb 2026
https://github.com/edinburgh-genome-foundry/dnafeaturesviewer
:eye: Python library to plot DNA sequence features (e.g. from Genbank files)
bioinformatics dna-visualization genbank molecular-biology synthetic-biology visualization
Last synced: 14 May 2025
https://github.com/biojava/biojava
:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.
bioinformatics genomics java parser-library pdb protein-data-bank protein-modification protein-sequences protein-structure sequence-alignment structural-bioinformatics structure-alignment
Last synced: 17 Dec 2025
https://github.com/ysig/grakel
A scikit-learn compatible library for graph kernels
bioinformatics chemoinformatics graph-classification graph-kernels graph-mining graph-similarity graph-similarity-algorithms scikit-learn
Last synced: 14 May 2025
https://github.com/ysig/GraKeL
A scikit-learn compatible library for graph kernels
bioinformatics chemoinformatics graph-classification graph-kernels graph-mining graph-similarity graph-similarity-algorithms scikit-learn
Last synced: 02 May 2025
https://github.com/lh3/bioawk
BWK awk modified for biological data
bioinformatics sequence-analysis
Last synced: 12 Apr 2025
https://github.com/jts/nanopolish
Signal-level algorithms for MinION data
bioinformatics c-plus-plus epigenetics genome-assembly methylation science
Last synced: 23 Jan 2026
https://github.com/fritzsedlazeck/sniffles
Structural variation caller using third generation sequencing
bioconda bioinformatics nanopore ngm-lr pacbio structural-variation structural-variations
Last synced: 14 May 2025
https://github.com/Starlitnightly/omicverse
A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
bioinformatics bulk-rna-seq omics single-cell
Last synced: 16 Mar 2025
https://github.com/plotly/dash-cytoscape
Interactive network visualization in Python and Dash, powered by Cytoscape.js
bioinformatics biopython computational-biology cytoscape cytoscapejs dash data-science graph-theory network-graph network-visualization plotly plotly-dash
Last synced: 20 Oct 2025
https://github.com/insitro/redun
Yet another redundant workflow engine
aws bioinformatics data-engineering data-science docker etl gcp ml python workflow-engine
Last synced: 23 Feb 2026
https://github.com/soedinglab/hh-suite
Remote protein homology detection suite.
alignment bioinformatics cpp hh-suite hhblits hhpred hhsearch opensource profile-profile-search profile-search protein-structure sequence-search simd viterbi
Last synced: 14 Apr 2025
https://github.com/gamcil/clinker
Gene cluster comparison figure generator
bioinformatics d3js python visualization
Last synced: 10 Apr 2025
https://github.com/cdk/cdk
The Chemistry Development Kit
bioinformatics blueobelisk cheminformatics chemistry code4lib java
Last synced: 21 Oct 2025
https://github.com/marcelm/cutadapt
Cutadapt removes adapter sequences from sequencing reads
Last synced: 14 May 2025
https://github.com/martinsos/edlib
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
alignment-path bioinformatics c-plus-plus edit-distance levehnstein-distance library python sequence-alignment
Last synced: 10 Apr 2025
https://github.com/Martinsos/edlib
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
alignment-path bioinformatics c-plus-plus edit-distance levehnstein-distance library python sequence-alignment
Last synced: 30 Mar 2025
https://github.com/chhylp123/hifiasm
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
bioinformatics denovo-assembly genomics hifi-read pacbio
Last synced: 05 May 2025
https://github.com/benjjneb/dada2
Accurate sample inference from amplicon data with single nucleotide resolution
amplicon bioconductor bioinformatics metabarcoding metagenomics microbiome taxonomy
Last synced: 18 Feb 2026
https://github.com/plotly/dash-bio
Open-source bioinformatics components for Dash
Last synced: 20 Oct 2025
https://github.com/sourmash-bio/sourmash
Quickly search, compare, and analyze genomic and metagenomic data sets.
bioinformatics fracminhash hacktoberfest kmer minhash python rust scaled-minhash sketching sourmash taxonomic-classification taxonomic-profiling
Last synced: 21 Oct 2025
https://github.com/nicgirault/circosjs
d3 library to build circular graphs
big-data bigdata bioinformatics bioinformatics-data circos circos-graphs circular d3js javascript
Last synced: 09 Apr 2025
https://github.com/nicgirault/circosJS
d3 library to build circular graphs
big-data bigdata bioinformatics bioinformatics-data circos circos-graphs circular d3js javascript
Last synced: 07 May 2025
https://github.com/tseemann/snippy
:scissors: :zap: Rapid haploid variant calling and core genome alignment
bacteria bioinformatics fastq-analysis genomics haploid indel-discovery snps variant-calling vcf
Last synced: 12 Apr 2025
https://github.com/plotly/react-cytoscapejs
React component for Cytoscape.js network visualisations
bioinformatics network-graph react
Last synced: 15 May 2025
https://github.com/oschwengers/bakta
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
annotation bacteria bacterial-genomes bioinformatics genome-annotation mag metagenome-assembled-genomes microbial-genomics plasmids
Last synced: 14 May 2025
https://github.com/plotly/dash.jl
Dash for Julia - A Julia interface to the Dash ecosystem for creating analytic web applications in Julia. No JavaScript required.
bioinformatics charting dash dashboard data-science data-visualization finance gui-framework julia modeling no-javascript no-vba plotly plotly-dash productivity react technical-computing web-app
Last synced: 23 Oct 2025
https://github.com/crazyhottommy/bioinformatics-one-liners
Bioinformatics one liners from Ming Tang
Last synced: 05 Apr 2025
https://github.com/PoisonAlien/maftools
Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
bioinformatics cancer-genome-atlas cancer-genomics genomics maf-files r tcga
Last synced: 25 Nov 2025
