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The Top 23 Bioinformatics Genome Open Source Projects

Open source projects categorized as Bioinformatics Genome
Categories > Data Processing > Bioinformatics
Categories > Science > Genome
Deepvariant ⭐ 2,978
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
Gatk ⭐ 1,576
Official code repository for GATK versions 4 and up
dependent packages 2total releases 46most recent commit a month ago
Hail ⭐ 905
Cloud-native genomic dataframes and batch computing
dependent packages 17total releases 146most recent commit 3 months agopypi hail} Downloads
Ncbi Genome Download ⭐ 784
Scripts to download genomes from the NCBI FTP servers
dependent packages 6total releases 25most recent commit 9 months agopypi ncbi-genome-download} Downloads
Jcvi ⭐ 650
Python library to facilitate genome assembly, annotation, and comparative genomics
dependent packages 1total releases 97most recent commit 4 months agopypi jcvi} Downloads
Bowtie2 ⭐ 594
A fast and sensitive gapped read aligner
most recent commit 3 months ago
Nanopolish ⭐ 496
Signal-level algorithms for MinION data
most recent commit 8 months ago
Sniffles ⭐ 479
Structural variation caller using third generation sequencing
total releases 8most recent commit 3 months ago
Hifiasm ⭐ 443
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
most recent commit 3 months ago
Megahit ⭐ 442
Ultra-fast and memory-efficient (meta-)genome assembler
most recent commit a year ago
Jbrowse ⭐ 437
Full-featured and stable genome browser built with JavaScript and HTML5.
dependent packages 2total releases 30most recent commit a year agonpm @gmod/jbrowse} Downloads
Snippy ⭐ 408
✂️ ⚡ Rapid haploid variant calling and core genome alignment
most recent commit 6 months ago
Gtdbtk ⭐ 383
GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
dependent packages 1total releases 48most recent commit 5 months agopypi gtdbtk} Downloads
Bakta ⭐ 365
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
total releases 37most recent commit 3 months ago
Bismark ⭐ 335
A tool to map bisulfite converted sequence reads and determine cytosine methylation states
most recent commit 7 months ago
Quast ⭐ 327
Genome assembly evaluation tool
most recent commit 7 months ago
Sarek ⭐ 299
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
most recent commit 3 months ago
Awesome Cancer Variant Databases ⭐ 284
A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.
most recent commit 6 months ago
Hap.py ⭐ 283
Haplotype VCF comparison tools
most recent commit 2 years ago
Karyoploter ⭐ 278
karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome
most recent commit 3 months ago
Abyss ⭐ 276
🔬 Assemble large genomes using short reads
most recent commit 8 months ago
Genometools ⭐ 261
GenomeTools genome analysis system.
most recent commit 5 months ago
Ribbon ⭐ 249
A genome browser that shows long reads and complex variants better
most recent commit a year ago
The 10 Most Depended On Bioinformatics Genome Open Source Projects
Pyfastx ⭐ 211
a python package for fast random access to sequences from plain and gzipped FASTA/Q files
dependent packages 20total releases 68latest release November 25, 2023most recent commit 5 months agopypi pyfastx} Downloads
Hail ⭐ 905
Cloud-native genomic dataframes and batch computing
dependent packages 17total releases 146latest release October 30, 2023most recent commit 3 months agopypi hail} Downloads
Pyrodigal ⭐ 111
Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!
dependent packages 14total releases 60latest release November 27, 2023most recent commit 3 months agopypi pyrodigal} Downloads
Bio ⭐ 86
A lightweight and high-performance bioinformatics package in Golang
dependent packages 13total releases 32latest release November 11, 2023most recent commit 3 months ago
Hgvs ⭐ 226
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
dependent packages 12total releases 104latest release November 21, 2022most recent commit 3 months agopypi hgvs} Downloads
Ncbi Genome Download ⭐ 784
Scripts to download genomes from the NCBI FTP servers
dependent packages 6total releases 25latest release July 28, 2023most recent commit 9 months agopypi ncbi-genome-download} Downloads
Gatk ⭐ 1,576
Official code repository for GATK versions 4 and up
dependent packages 2total releases 46latest release March 16, 2023most recent commit a month ago
Jbrowse ⭐ 437
Full-featured and stable genome browser built with JavaScript and HTML5.
dependent packages 2total releases 30latest release July 12, 2019most recent commit a year agonpm @gmod/jbrowse} Downloads
The 10 Latest Releases In Bioinformatics Genome Open Source Projects
Bakta ⭐ 365
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
total releases 37latest release November 29, 2023most recent commit 3 months ago
Pyrodigal ⭐ 111
Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!
dependent packages 14total releases 60latest release November 27, 2023most recent commit 3 months agopypi pyrodigal} Downloads
Pyfastx ⭐ 211
a python package for fast random access to sequences from plain and gzipped FASTA/Q files
dependent packages 20total releases 68latest release November 25, 2023most recent commit 5 months agopypi pyfastx} Downloads
Genet ⭐ 8
Python library for genome editing and CRISPR research
total releases 37latest release November 24, 2023most recent commit 3 months ago
Bio ⭐ 86
A lightweight and high-performance bioinformatics package in Golang
dependent packages 13total releases 32latest release November 11, 2023most recent commit 3 months ago
Genomehubs ⭐ 12
Search and explore genomic metadata, Earth BioGenome Project progress and assembly features
total releases 128latest release November 09, 2023most recent commit 4 months ago
Teloclip ⭐ 26
A tool for the recovery of unassembled telomeres from soft-clipped read alignments.
total releases 3latest release November 06, 2023most recent commit 3 months ago
Telomeric Identifier ⭐ 73
Identify and find telomeres, or telomeric repeats in a genome.
total releases 5latest release November 04, 2023most recent commit 5 months ago
Hail ⭐ 905
Cloud-native genomic dataframes and batch computing
dependent packages 17total releases 146latest release October 30, 2023most recent commit 3 months agopypi hail} Downloads
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