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The Top 23 Genomics Sequencing Open Source Projects

Open source projects categorized as Genomics Sequencing
Categories > Science > Genomics
Categories > Science > Sequencing
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 5 months ago
Gatk ⭐ 1,576
Official code repository for GATK versions 4 and up
dependent packages 2total releases 46most recent commit a month ago
Galaxy ⭐ 1,211
Data intensive science for everyone.
dependent packages 23total releases 30most recent commit 3 months agopypi galaxy-util} Downloads
Getting Started With Genomics Tools And Resources ⭐ 991
Unix, R and python tools for genomics and data science
most recent commit 3 months ago
Adam ⭐ 966
ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
dependent packages 17total releases 14most recent commit 3 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
Fgbio ⭐ 292
Tools for working with genomic and high throughput sequencing data.
total releases 16most recent commit 3 months ago
Truvari ⭐ 284
Structural variant toolkit for VCFs
total releases 23most recent commit 15 days ago
Htsjdk ⭐ 271
A Java API for high-throughput sequencing data (HTS) formats.
dependent packages 87total releases 78most recent commit 4 months ago
Sequenceserver ⭐ 259
Intuitive graphical web interface for running BLAST bioinformatics tool (i.e. have your own custom NCBI BLAST site!)
total releases 68most recent commit 3 months ago
Comp Genomics Class ⭐ 236
Code and examples for JHU Computational Genomics class
most recent commit 3 years ago
Hgvs ⭐ 226
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
dependent packages 12total releases 104most recent commit 3 months agopypi hgvs} Downloads
Roary ⭐ 219
Rapid large-scale prokaryote pan genome analysis
total releases 83most recent commit 2 years ago
Miso Lims ⭐ 214
MISO: An open-source LIMS for NGS sequencing centres
most recent commit 3 months ago
Smudgeplot ⭐ 200
Inference of ploidy and heterozygosity structure using whole genome sequencing data
most recent commit 3 months ago
Circlator ⭐ 193
A tool to circularize genome assemblies
total releases 33most recent commit 8 months ago
Artemis ⭐ 191
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 a year ago
Wgsim ⭐ 188
Reads simulator
most recent commit 3 years ago
Snp Sites ⭐ 173
Finds SNP sites from a multi-FASTA alignment file
most recent commit 3 years ago
Genomics ⭐ 154
A collection of scripts and notes related to genomics and bioinformatics
most recent commit 2 years ago
Readfish ⭐ 152
CLI tool for flexible and fast adaptive sampling on ONT sequencers
total releases 9most recent commit 4 months ago
Genomicsqlite ⭐ 146
Genomics Extension for SQLite
dependent packages 1total releases 21most recent commit 3 months agopypi genomicsqlite} Downloads
Ariba ⭐ 135
Antimicrobial Resistance Identification By Assembly
dependent packages 1total releases 54most recent commit a year agopypi ariba} Downloads
The 10 Most Depended On Genomics Sequencing Open Source Projects
Htsjdk ⭐ 271
A Java API for high-throughput sequencing data (HTS) formats.
dependent packages 87total releases 78latest release October 13, 2023most recent commit 4 months ago
Galaxy ⭐ 1,211
Data intensive science for everyone.
dependent packages 23total releases 30latest release December 08, 2023most recent commit 3 months agopypi galaxy-util} Downloads
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
Biocommons.seqrepo ⭐ 34
non-redundant, compressed, journalled, file-based storage for biological sequences
dependent packages 12total releases 42latest release November 13, 2023most recent commit 3 months agopypi biocommons.seqrepo} Downloads
Bioutils ⭐ 16
provides common tools and lookup tables used primarily by the hgvs and uta packages
dependent packages 8total releases 62latest release July 10, 2023most recent commit 3 months agopypi bioutils} Downloads
Fastaq ⭐ 45
Python3 scripts to manipulate FASTA and FASTQ files
dependent packages 7total releases 21latest release February 19, 2018most recent commit 2 years agopypi pyfastaq} 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
Genomicsqlite ⭐ 146
Genomics Extension for SQLite
dependent packages 1total releases 21latest release December 28, 2022most recent commit 3 months agopypi genomicsqlite} Downloads
Ariba ⭐ 135
Antimicrobial Resistance Identification By Assembly
dependent packages 1total releases 54latest release September 07, 2020most recent commit a year agopypi ariba} Downloads
The 10 Latest Releases In Genomics Sequencing Open Source Projects
Galaxy ⭐ 1,211
Data intensive science for everyone.
dependent packages 23total releases 30latest release December 08, 2023most recent commit 3 months agopypi galaxy-util} Downloads
Biocommons.seqrepo ⭐ 34
non-redundant, compressed, journalled, file-based storage for biological sequences
dependent packages 12total releases 42latest release November 13, 2023most recent commit 3 months agopypi biocommons.seqrepo} Downloads
Htsjdk ⭐ 271
A Java API for high-throughput sequencing data (HTS) formats.
dependent packages 87total releases 78latest release October 13, 2023most recent commit 4 months ago
Readfish ⭐ 152
CLI tool for flexible and fast adaptive sampling on ONT sequencers
total releases 9latest release October 12, 2023most recent commit 4 months ago
Sandy ⭐ 14
A straightforward and complete next-generation sequencing read simulator
total releases 9latest release September 19, 2023most recent commit 5 months ago
Truvari ⭐ 284
Structural variant toolkit for VCFs
total releases 23latest release August 07, 2023most recent commit 15 days ago
Bioutils ⭐ 16
provides common tools and lookup tables used primarily by the hgvs and uta packages
dependent packages 8total releases 62latest release July 10, 2023most recent commit 3 months agopypi bioutils} Downloads
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