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The Top 4,986 Genome Open Source Projects

Categories > Science > Genome
Iamdinosaur ⭐ 2,760
🦄 An Artificial Inteligence to teach Google's Dinosaur to jump cactus
most recent commit 4 years ago
Deepvariant ⭐ 2,457
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
most recent commit 4 months ago
Ncov ⭐ 1,290
Nextstrain build for novel coronavirus SARS-CoV-2
most recent commit 2 days ago
Star ⭐ 1,267
RNA-seq aligner
most recent commit a month ago
Gatk ⭐ 1,258
Official code repository for GATK versions 4 and up
dependent packages 2total releases 44most recent commit 5 days ago
Bottom Up Attention ⭐ 979
Bottom-up attention model for image captioning and VQA, based on Faster R-CNN and Visual Genome
most recent commit a year ago
Ai Programmer ⭐ 965
Using artificial intelligence and genetic algorithms to automatically write programs. Tutorial: http://www.primaryobjects.com/cms/article149
most recent commit 2 years ago
Vg ⭐ 832
tools for working with genome variation graphs
most recent commit 19 days ago
Hail ⭐ 810
Scalable genomic data analysis.
most recent commit 5 days ago
Genome ⭐ 778
A simple, type safe, failure driven mapping library for serializing JSON to models in Swift 3.0 (Supports Linux)
total releases 15most recent commit 4 years ago
Bedtools2 ⭐ 757
bedtools - the swiss army knife for genome arithmetic
most recent commit a month ago
Applied Computational Genomics ⭐ 738
Applied Computational Genomics Course at UU: Spring 2020
most recent commit 3 months ago
Ncbi Genome Download ⭐ 576
Scripts to download genomes from the NCBI FTP servers
dependent packages 3total releases 23most recent commit 7 months agopypi ncbi-genome-download} Downloads
Salmon ⭐ 557
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
most recent commit 12 days ago
Pygenometracks ⭐ 550
python module to plot beautiful and highly customizable genome browser tracks
most recent commit 3 months ago
Canu ⭐ 528
A single molecule sequence assembler for genomes large and small.
most recent commit 12 days ago
Jcvi ⭐ 509
Python library to facilitate genome assembly, annotation, and comparative genomics
total releases 76most recent commit 6 days ago
Ban Vqa ⭐ 478
Bilinear attention networks for visual question answering
most recent commit 7 months ago
Mosdepth ⭐ 478
fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
most recent commit 2 months ago
Bowtie2 ⭐ 453
A fast and sensitive gapped read aligner
most recent commit a month ago
Biotools ⭐ 446
A list of useful bioinformatics resources
most recent commit 4 months ago
Nanopolish ⭐ 422
Signal-level algorithms for MinION data
most recent commit a month ago
Prokka ⭐ 415
⚡️ ♒️ Rapid prokaryotic genome annotation
most recent commit 2 years ago
Jbrowse ⭐ 401
A modern genome browser built with JavaScript and HTML5.
total releases 30most recent commit a year ago
Awesome Genome Visualization ⭐ 396
A list of interesting genome browser or genome-browser-like implementations
most recent commit a day ago
Megahit ⭐ 387
Ultra-fast and memory-efficient (meta-)genome assembler
most recent commit 3 months ago
Pytorch Neat ⭐ 387
most recent commit 2 years ago
Unicycler ⭐ 374
hybrid assembly pipeline for bacterial genomes
most recent commit 5 months ago
Eggnog Mapper ⭐ 365
Fast genome-wide functional annotation through orthology assignment
most recent commit 20 days ago
Represent Map ⭐ 360
Visualize your startup community on a custom Google map. Based on the code for http://represent.la
most recent commit 4 years ago
Dna2json ⭐ 357
Formats your genome file as JSON
dependent packages 2total releases 14most recent commit 5 years agonpm dna2json} Downloads
Samplot ⭐ 354
Plot structural variant signals from many BAMs and CRAMs
total releases 3most recent commit 2 months ago
Hisat2 ⭐ 345
Graph-based alignment (Hierarchical Graph FM index)
most recent commit 4 months ago
Sniffles ⭐ 323
Structural variation caller using third generation sequencing
total releases 6most recent commit 3 months ago
Na12878 ⭐ 321
Data and analysis for NA12878 genome on nanopore
most recent commit 4 months ago
Hic_tools ⭐ 319
A collection of tools for Hi-C data analysis
most recent commit 21 days ago
Awesome Crispr ⭐ 294
List of software/websites/databases/other stuff for genome engineering
most recent commit 3 months ago
Multineat ⭐ 289
Portable NeuroEvolution Library
most recent commit 3 years ago
Speedseq ⭐ 285
A flexible framework for rapid genome analysis and interpretation
most recent commit 4 years ago
Hap.py ⭐ 283
Haplotype VCF comparison tools
most recent commit 7 months ago
Rsem ⭐ 279
RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
most recent commit a year ago
Snakepipes ⭐ 277
Customizable workflows based on snakemake and python for the analysis of NGS data
most recent commit 4 months ago
Vcftools ⭐ 273
A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.
most recent commit 2 years ago
Gemini ⭐ 272
a lightweight db framework for exploring genetic variation.
most recent commit 2 years ago
Mummer ⭐ 264
Mummer alignment tool
most recent commit 2 years ago
Gtdbtk ⭐ 259
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
dependent packages 1total releases 37most recent commit a month agopypi gtdbtk} Downloads
Atac Seq Pipeline ⭐ 257
ENCODE ATAC-seq pipeline
most recent commit 22 days ago
Bismark ⭐ 257
A tool to map bisulfite converted sequence reads and determine cytosine methylation states
most recent commit 18 days ago
Genomepy ⭐ 257
genes and genomes at your fingertips
dependent packages 1total releases 32most recent commit 13 days agopypi genomepy} Downloads
Metawrap ⭐ 253
MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
most recent commit a month ago
Flam3 ⭐ 249
the original fractal flame renderer and genetic language
most recent commit 2 years ago
Abyss ⭐ 244
🔬 Assemble large genomes using short reads
most recent commit 13 days ago
Quast ⭐ 243
Genome assembly evaluation tool
most recent commit a month ago
Cactus ⭐ 243
Official home of genome aligner based upon notion of Cactus graphs
most recent commit 4 days ago
Pygeno ⭐ 242
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
total releases 18most recent commit 2 years ago
Fastani ⭐ 235
Fast Whole-Genome Similarity (ANI) Estimation
most recent commit 3 days ago
Ngmlr ⭐ 230
NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations
most recent commit a year ago
Ideogram ⭐ 227
Chromosome visualization for the web
dependent packages 5total releases 67most recent commit 6 days agonpm ideogram} Downloads
Genometools ⭐ 226
GenomeTools genome analysis system.
most recent commit 2 months ago
Karyoploter ⭐ 222
karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome
most recent commit 6 months ago
Roary ⭐ 219
Rapid large-scale prokaryote pan genome analysis
total releases 83most recent commit 2 months ago
Ribbon ⭐ 215
A genome browser that shows long reads and complex variants better
most recent commit 2 months ago
Flowcraft ⭐ 214
FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. 🐳📦
total releases 18most recent commit 2 years ago
Checkm ⭐ 214
Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
most recent commit 2 months ago
Liftoff ⭐ 209
An accurate GFF3/GTF lift over pipeline
most recent commit 5 months ago
Dalliance ⭐ 208
Interactive web-based genome browser.
dependent packages 1total releases 1most recent commit 3 years agonpm dalliance} Downloads
Snippy ⭐ 205
✂️ ⚡️ Rapid haploid variant calling and core genome alignment
most recent commit 2 years ago
Ngsplot ⭐ 205
Quick mining and visualization of NGS data by integrating genomic databases
most recent commit 6 months ago
Pcgr ⭐ 204
Personal Cancer Genome Reporter (PCGR)
most recent commit 8 days ago
Visual_genome_python_driver ⭐ 204
A python wrapper for the Visual Genome API
total releases 3most recent commit 3 years ago
Giggle ⭐ 203
Interval data structure
most recent commit 2 months ago
Funannotate ⭐ 202
Eukaryotic Genome Annotation Pipeline
total releases 11most recent commit 4 days ago
Edta ⭐ 199
Extensive de-novo TE Annotator
most recent commit 13 days ago
Trycycler ⭐ 198
A tool for generating consensus long-read assemblies for bacterial genomes
most recent commit 22 days ago
Basset ⭐ 195
Convolutional neural network analysis for predicting DNA sequence activity.
most recent commit 2 years ago
Pgap ⭐ 192
NCBI Prokaryotic Genome Annotation Pipeline
most recent commit a month ago
Rgi ⭐ 191
Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.
most recent commit 8 days ago
Chromosomemappings ⭐ 189
This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.
most recent commit 9 months ago
Hifiasm ⭐ 185
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
most recent commit 10 months ago
Ragtag ⭐ 185
Tools for fast and flexible genome assembly scaffolding and improvement
total releases 7most recent commit 7 months ago
Pggb ⭐ 179
the pangenome graph builder
most recent commit 2 days ago
Chip Seq Pipeline2 ⭐ 176
ENCODE ChIP-seq pipeline
most recent commit 22 days ago
Genvisr ⭐ 175
Genome data visualizations
most recent commit 5 months ago
Awesome Cancer Variant Databases ⭐ 173
A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.
most recent commit 3 years ago
Sarek ⭐ 171
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
most recent commit 14 days ago
Centrifuge ⭐ 171
Classifier for metagenomic sequences
most recent commit 6 months ago
Masurca ⭐ 169
most recent commit 4 days ago
Kubegene ⭐ 169
KubeGene - A turn-key Genome Sequencing workflow management framework
most recent commit 2 years ago
Hgvs ⭐ 169
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
dependent packages 10total releases 101most recent commit a month agopypi hgvs} Downloads
Gemma ⭐ 168
Genome-wide Efficient Mixed Model Association
most recent commit 5 months ago
Kent ⭐ 166
UCSC Genome Browser source tree. Stable branch: "beta".
most recent commit 2 hours ago
Augustus ⭐ 166
Genome annotation with AUGUSTUS
most recent commit 4 months ago
Aligngraph ⭐ 165
Algorithm for secondary de novo genome assembly guided by closely related references
most recent commit 2 years ago
Bactopia ⭐ 164
A flexible pipeline for complete analysis of bacterial genomes
most recent commit a month ago
Artemis ⭐ 163
Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
most recent commit 3 months ago
Biomartr ⭐ 162
Genomic Data Retrieval with R
dependent packages 2total releases 16most recent commit 2 months ago
Doc Annovar ⭐ 159
Documentation for the ANNOVAR software
most recent commit 3 months ago
Braker ⭐ 159
BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes
most recent commit 5 months ago
Mashmap ⭐ 157
A fast approximate aligner for long DNA sequences
most recent commit a year ago
Asciigenome ⭐ 156
Text Only Genome Viewer!
most recent commit 2 years ago
1-100 of 4,986 projects
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