genomics
There are 2480 repositories under genomics topic.
biopython/biopython
Official git repository for Biopython (originally converted from CVS)
google/deepvariant
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
lh3/minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences
broadinstitute/gatk
Official code repository for GATK versions 4 and up
lh3/bwa
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
galaxyproject/galaxy
Data intensive science for everyone.
greenelab/deep-review
A collaboratively written review paper on deep learning, genomics, and precision medicine
vgteam/vg
tools for working with genome variation graphs
bigdatagenomics/adam
ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
hail-is/hail
Cloud-native genomic dataframes and batch computing
kblin/ncbi-genome-download
Scripts to download genomes from the NCBI FTP servers
MareesAT/GWA_tutorial
A comprehensive tutorial about GWAS and PRS
google/nucleus
Python and C++ code for reading and writing genomics data.
tanghaibao/goatools
Python library to handle Gene Ontology (GO) terms
tanghaibao/jcvi
Python library to facilitate genome assembly, annotation, and comparative genomics
seq-lang/seq
A high-performance, Pythonic language for bioinformatics
bwa-mem2/bwa-mem2
The next version of bwa-mem
deeptools/deepTools
Tools to process and analyze deep sequencing data.
moshi4/pyCirclize
Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)
BenLangmead/bowtie2
A fast and sensitive gapped read aligner
vcflib/vcflib
C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
biojava/biojava
:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.
voutcn/megahit
Ultra-fast and memory-efficient (meta-)genome assembler
flowhub-team/awesome-omics
A collection of awesome things regarding all omics.
eggnogdb/eggnog-mapper
Fast genome-wide functional annotation through orthology assignment
HazyResearch/hyena-dna
Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena
chhylp123/hifiasm
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
lindenb/jvarkit
Java utilities for Bioinformatics
GMOD/jbrowse
JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.
mdshw5/pyfaidx
Efficient pythonic random access to fasta subsequences
tseemann/snippy
:scissors: :zap: Rapid haploid variant calling and core genome alignment
nanoporetech/dorado
Oxford Nanopore's Basecaller
priyank-purohit/PostGUI
A React web application to query and share any PostgreSQL database.
PoisonAlien/maftools
Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
pyranges/pyranges
Performant Pythonic GenomicRanges
instadeepai/nucleotide-transformer
š§¬ Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics