genome

ivanseidel/IAMDinosaur

🦄 An Artificial Inteligence to teach Google's Dinosaur to jump cactus

broadinstitute/gatk

Official code repository for GATK versions 4 and up

primaryobjects/AI-Programmer

Using artificial intelligence and genetic algorithms to automatically write programs. Tutorial: http://www.primaryobjects.com/cms/article149

brentp/mosdepth

fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing

jerryji1993/DNABERT

DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

vanheeringen-lab/genomepy

genes and genomes at your fingertips

tariqdaouda/pyGeno

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

bcgsc/abyss

:microscope: Assemble large genomes using short reads

bernatgel/karyoploteR

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

genometools/genometools

GenomeTools genome analysis system.

Gaius-Augustus/Augustus

Genome annotation with AUGUSTUS

MariaNattestad/Ribbon

A genome browser that shows long reads and complex variants better

lmdu/pyfastx

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

flowhub-team/WholeGenomeSequencing-WGS

Whole Genome Sequencing analysis, WGS analysis

alekseyzimin/masurca

bcgsc/NanoSim

Nanopore sequence read simulator

aquaskyline/SOAPdenovo2

Next generation sequencing reads de novo assembler.

ropensci/biomartr

Genomic Data Retrieval with R

Nextomics/NextPolish

Fast and accurately polish the genome generated by long reads.

MAGICS-LAB/DNABERT_2

[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome

broadinstitute/viral-ngs

Viral genomics analysis pipelines

genome-spy/genome-spy

A visualization grammar and GPU-accelerated toolkit for genomic data

HICAI-ZJU/Scientific-LLM-Survey

Scientific Large Language Models: A Survey on Biological & Chemical Domains

aehrc/VariantSpark

machine learning for genomic variants

pirovc/genome_updater

Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy

althonos/pyrodigal

Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!

nf-core/eager

A fully reproducible and state-of-the-art ancient DNA analysis pipeline

cslarsen/arv

A fast 23andMe DNA parser and inferrer for Python

mentatpsi/OSGenome

An Open Source Web Application for Genetic Data (SNPs) using 23AndMe and Data Crawling Technologies

COMBINE-lab/pufferfish

An efficient index for the colored, compacted, de Bruijn graph

DECIPHER-genomics/Genoverse

HTML5 scrollable genome browser

tolkit/telomeric-identifier

Identify and find telomeres, or telomeric repeats in a genome.

google/deepsomatic

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

genotoul-bioinfo/dgenies

Dotplot large Genomes in an Interactive, Efficient and Simple way

bcgsc/arcs

🌈Scaffold genome sequence assemblies using linked or long read sequencing data