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An open API service indexing awesome lists of open source software.

Projects in Awesome Lists tagged with genomics

A curated list of projects in awesome lists tagged with genomics .

https://github.com/k-dense-ai/scientific-agent-skills

Turn any AI agent into an AI Scientist. The #1 Agent Skills library for science, used by 160,000+ scientists worldwide. 138 ready-to-use skills plus 100+ scientific databases covering biology, chemistry, medicine, and drug discovery. Compatible with Cursor, Claude Code, Codex, Antigravity, and the open Agent Skills standard.

agent-skills ai-scientist bioinformatics chemoinformatics claude claude-skills claudecode clinical-research computational-biology data-analysis drug-discovery genomics materials-science metabolomics proteomics scientific-computing scientific-visualization

Last synced: 28 May 2026

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/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/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/vgteam/vg

tools for working with genome variation graphs

dna genome-graph genomics graph variation-graph

Last synced: 09 Feb 2026

https://github.com/greenelab/deep-review

A collaboratively written review paper on deep learning, genomics, and precision medicine

deep-learning genomics manubot manuscript neural-networks review

Last synced: 27 Jan 2026

https://greenelab.github.io/deep-review/

A collaboratively written review paper on deep learning, genomics, and precision medicine

deep-learning genomics manubot manuscript neural-networks review

Last synced: 16 Mar 2025

https://github.com/pachterlab/gget

🧬 gget enables efficient querying of genomic reference databases

alphafold alphafold2 archs4 blast databases enrichment-analysis enrichr ensembl genomics gget ncbi proteomics reference rna-seq transcriptomics uniprot

Last synced: 27 Feb 2026

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/bigdatagenomics/adam

ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.

avro big-data bioinformatics genomics java parquet python r scala spark

Last synced: 19 Oct 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/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/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/hazyresearch/hyena-dna

Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena

foundation-models genomics language-models

Last synced: 13 Apr 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/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/ekg/vcflib

C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

genomics genotyping haplotypecaller variant-calling vcf-manipulation

Last synced: 20 Apr 2025

https://github.com/nanoporetech/dorado

Oxford Nanopore's Basecaller

basecalling genomics libtorch nanopore

Last synced: 15 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/vcflib/vcflib

C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings

genomics genotyping haplotypecaller variant-calling vcf-manipulation

Last synced: 25 Feb 2026

https://github.com/instadeepai/nucleotide-transformer

🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics

deep-learning dna genomics language-model nucleotide transformer

Last synced: 03 Nov 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/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/pyranges/pyranges

Performant Pythonic GenomicRanges

data-structures genomicranges genomics pandas python

Last synced: 03 Apr 2026

https://github.com/lucidrains/enformer-pytorch

Implementation of Enformer, Deepmind's attention network for predicting gene expression, in Pytorch

artificial-intelligence attention-mechanism deep-learning dna-sequences gene-expression genomics transformer

Last synced: 15 May 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

https://github.com/aidenlab/juicer

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

3d-genome 3d-genome-browser bioinformatics genomics hi-c ngs

Last synced: 26 Jan 2026

https://github.com/gmod/jbrowse

JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.

bioinformatics biology genome-annotation genome-browser genomics protein-annotation

Last synced: 14 May 2025

https://github.com/mdshw5/pyfaidx

Efficient pythonic random access to fasta subsequences

bgzf bioinformatics dna fasta genomics indexing protein python samtools

Last synced: 14 May 2025

https://github.com/GMOD/jbrowse

JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.

bioinformatics biology genome-annotation genome-browser genomics protein-annotation

Last synced: 30 Mar 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: 14 May 2025

https://github.com/illumina/hap.py

Haplotype VCF comparison tools

bioinformatics genomics vcf vcf-comparison

Last synced: 04 Apr 2025

https://github.com/brentp/cyvcf2

cython + htslib == fast VCF and BCF processing

bioinformatics cython genomics htslib vcf

Last synced: 27 Jan 2026

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: 02 Apr 2026

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: 12 Feb 2026

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/pinellolab/dna-diffusion

🧬 Generative modeling of regulatory DNA sequences with diffusion probabilistic models 💨

deep-learning diffusion-models diffusion-probabilistic-models generative-model genomics regulatory-genomics stable-diffusion

Last synced: 15 May 2025

https://github.com/HKU-BAL/Clair3

Clair3 - Symphonizing pileup and full-alignment for deep learning-based long-read variant calling

computational-biology deep-learning genomics illumina long-reads nanopore ont-data ont-models pacbio variant-calling variant-detection

Last synced: 11 Jun 2026

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/hku-bal/clair3

Clair3 - Symphonizing pileup and full-alignment for deep learning-based long-read variant calling

computational-biology deep-learning genomics illumina long-reads nanopore ont-data ont-models pacbio variant-calling variant-detection

Last synced: 27 Apr 2026

https://github.com/lh3/miniasm

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

bioinformatics denovo-assembly genomics

Last synced: 27 Jan 2026

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: 10 Oct 2025

https://github.com/higlass/higlass

Fast, flexible and extensible genome browser.

gehlenborglab genomics hi-c higlass visualization

Last synced: 15 May 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/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: 04 Feb 2026

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: 17 Apr 2026

https://github.com/nvidia-genomics-research/genomeworks

SDK for GPU accelerated genome assembly and analysis

alignment cuda genomics gpu mapping nvidia partial-order-alignment poa python-api

Last synced: 06 Apr 2026

https://github.com/google/deepsomatic

DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only sequencing data.

bioinformatics deep-learning deepsomatic dna genome genomics machine science sequencing somatic-mutations somatic-variants

Last synced: 06 Mar 2026

https://github.com/NVIDIA-Genomics-Research/GenomeWorks

SDK for GPU accelerated genome assembly and analysis

alignment cuda genomics gpu mapping nvidia partial-order-alignment poa python-api

Last synced: 09 May 2025

https://github.com/miso-lims/miso-lims

MISO: An open-source LIMS for NGS sequencing centres

docker genomics lims

Last synced: 12 Feb 2026

https://github.com/biocommons/hgvs

Python library to parse, format, validate, normalize, and map sequence variants according to HGVS Nomenclature (https://hgvs-nomenclature.org/).

bioinformatics genome-analysis genomics hgvs sequencing transcript variant-analysis variation

Last synced: 11 Mar 2026

https://github.com/samtools/htsjdk

A Java API for high-throughput sequencing data (HTS) formats.

bam cram dna fasta genomics java java-api ngs sam sequencing vcf

Last synced: 14 May 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: 15 May 2025

https://github.com/marianattestad/ribbon

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

bioinformatics genome genomics visualization

Last synced: 16 May 2025

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

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

bioinformatics genomics jbrowse visualization

Last synced: 03 Apr 2026

https://github.com/lh3/wgsim

Reads simulator

bioinformatics genomics

Last synced: 09 Apr 2025

https://github.com/projectglow/glow

An open-source toolkit for large-scale genomic analysis

delta genomics gwas machine-learning population-genetics regression spark

Last synced: 21 Oct 2025

https://github.com/KamilSJaron/smudgeplot

Inference of ploidy and heterozygosity structure using whole genome sequencing data

bioinformatics genomics kmer

Last synced: 21 Jul 2025

https://github.com/brentp/slivar

genetic variant expressions, annotation, and filtering for great good.

genomics rare-disease rare-variant-analysis variant-analysis variant-interpretation

Last synced: 26 Jan 2026

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/kundajelab/dragonn

A toolkit to learn how to model and interpret regulatory sequence data using deep learning.

deep-learning genomics

Last synced: 27 Jan 2026

https://github.com/knausb/vcfr

Tools to work with variant call format files

genomics population-genetics population-genomics rcpp rstats vcf-data visualization

Last synced: 22 Oct 2025

https://kundajelab.github.io/dragonn/

A toolkit to learn how to model and interpret regulatory sequence data using deep learning.

deep-learning genomics

Last synced: 10 May 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/BenLangmead/bowtie

An ultrafast memory-efficient short read aligner

bioinformatics c-plus-plus genomics read-aligners

Last synced: 15 Mar 2025

https://github.com/songlab-cal/gpn

Genomic Pre-trained Network

dna genomics language-model variant-effect-prediction

Last synced: 07 May 2025

https://github.com/brentp/smoove

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

genomics lumpy structural-variation

Last synced: 04 Apr 2025

https://github.com/assemblerflow/flowcraft

FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. :whale::package:

bacterial genomics nextflow pipeline

Last synced: 14 Jan 2026

https://github.com/linsalrob/computationalgenomicsmanual

Robs manual for the computational genomics and bioinformatics class.

bioinformatics genomics online-class

Last synced: 13 Apr 2025

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

Robs manual for the computational genomics and bioinformatics class.

bioinformatics genomics online-class

Last synced: 06 May 2025

https://github.com/mahmoodlab/PORPOISE

Pan-Cancer Integrative Histology-Genomic Analysis via Multimodal Deep Learning - Cancer Cell

genomics histology mahmoodlab pan-cancer-analysis wsi-images

Last synced: 09 May 2026

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