genomics

There are 207 repositories under genomics topic.

biopython / biopython
Official git repository for Biopython (originally converted from CVS)
bioinformatics biopython dna genomics phylogenetics protein protein-structure python sequence-alignment
Language:Python 4395
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
Language:Python 3240
lh3 / minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences
bioinformatics sequence-alignment spliced-alignment genomics
Language:C 1814
broadinstitute / gatk
Official code repository for GATK versions 4 and up
genomics spark science dna ngs sequencing genome bioinformatics gatk
Language:Java 1713
lh3 / bwa
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
bioinformatics fm-index genomics sequence-alignment
Language:C 1543
galaxyproject / galaxy
Data intensive science for everyone.
bioinformatics workflow genomics science sequencing ngs dna usegalaxy pipeline workflow-engine hacktoberfest
Language:Python 1414
greenelab / deep-review
A collaboratively written review paper on deep learning, genomics, and precision medicine
deep-learning genomics manubot manuscript neural-networks review
Language:HTML 1251
vgteam / vg
tools for working with genome variation graphs
variation-graph graph genome-graph genomics dna
Language:C++ 1122
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
Language:Scala 1003
hail
hail-is / hail
Cloud-native genomic dataframes and batch computing
bioinformatics genetics genomics gwas hail python software vcf
Language:Python 984
kblin / ncbi-genome-download
Scripts to download genomes from the NCBI FTP servers
ncbi bioinformatics download-genomes python biology genomics command-line genbank
Language:Python 956
MareesAT / GWA_tutorial
A comprehensive tutorial about GWAS and PRS
bioinformatics genetics genomics gwas plink population-stratification population-structure prs qc r unix
836
google / nucleus
Python and C++ code for reading and writing genomics data.
bioinformatics dna genomics tensorflow
Language:C++ 784
tanghaibao / goatools
Python library to handle Gene Ontology (GO) terms
bioinfomatics fdr fdr-benjamini fisher-tests gene-ontology gene-set-enrichment genomics goslim-terms holm-sidak sidak
Language:Python 782
pyCirclize
moshi4 / pyCirclize
Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)
bioinformatics circos matplotlib python chord-diagram comparative-genomics genomics genomics-visualization microbial-genomics visualization phylogenetic-trees data-visualization dataviz radar-chart
Language:Python 769
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
Language:Python 760
bwa-mem2 / bwa-mem2
The next version of bwa-mem
bioinformatics genomics sequence-alignment
Language:C++ 722
seq-lang / seq
A high-performance, Pythonic language for bioinformatics
bioinformatics compiler computational-biology domain-specific-language genomics programming-language python
Language:C++ 700
deeptools / deepTools
Tools to process and analyze deep sequencing data.
bioinformatics chip-seq genomics ngs python rna-seq
Language:Python 684
BenLangmead / bowtie2
A fast and sensitive gapped read aligner
bioinformatics c-plus-plus genomics read-aligners
Language:C++ 683
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
Language:C++ 621
voutcn / megahit
Ultra-fast and memory-efficient (meta-)genome assembler
bioinformatics metagenomics succinct data-structures genomics genome-assembly
Language:C++ 609
HazyResearch / hyena-dna
Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena
foundation-models genomics language-models
Language:Assembly 601
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
Language:Java 594
eggnogdb / eggnog-mapper
Fast genome-wide functional annotation through orthology assignment
annotations orthology-assignments functional-annotation genomics
Language:Python 571
chhylp123 / hifiasm
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
bioinformatics denovo-assembly genomics hifi-read pacbio
Language:C++ 549
flowhub-team / awesome-omics
A collection of awesome things regarding all omics.
awesome genomics ngs ngs-pipeline omics protein single-cell wgs-analysis
549
nanoporetech / dorado
Oxford Nanopore's Basecaller
basecalling genomics libtorch nanopore
Language:C++ 534
jvarkit
lindenb / jvarkit
Java utilities for Bioinformatics
bioinformatics biology genomics java next-generation-sequencing ngs science
Language:Java 485
instadeepai / nucleotide-transformer
🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics
deep-learning dna genomics language-model nucleotide transformer
Language:Python 479
tseemann / snippy
:scissors: :zap: Rapid haploid variant calling and core genome alignment
bacteria bioinformatics fastq-analysis genomics haploid indel-discovery snps variant-calling vcf
Language:Perl 478
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
Language:JavaScript 464
mdshw5 / pyfaidx
Efficient pythonic random access to fasta subsequences
bgzf bioinformatics dna fasta genomics indexing protein python samtools
Language:Python 460
maftools
PoisonAlien / maftools
Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
maf-files cancer-genomics cancer-genome-atlas tcga genomics bioinformatics r
Language:R 452
priyank-purohit / PostGUI
A React web application to query and share any PostgreSQL database.
reactjs postgresql postgres postgrest gui dashboard bioinformatics genomics data-sharing database database-gui database-as-a-service admin react-admin material-design data material-ui react typescript query-builder
Language:JavaScript 445
pyranges / pyranges
Performant Pythonic GenomicRanges
data-structures genomicranges genomics pandas python
Language:Python 443