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The Top 23 Next Generation Sequencing Open Source Projects

Open source projects categorized as Next Generation Sequencing
Categories > Next Generation Sequencing
Jvarkit ⭐ 440
Java utilities for Bioinformatics
most recent commit 5 months ago
Awosome Bioinformatics ⭐ 366
A curated list of resources for learning bioinformatics.
most recent commit 2 years 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
Kaiju ⭐ 236
Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
most recent commit 5 months 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 3 years ago
Roary ⭐ 219
Rapid large-scale prokaryote pan genome analysis
total releases 83most recent commit 2 years 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
Nextclade ⭐ 190
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
dependent packages 2total releases 52most recent commit 3 months agonpm @neherlab/nextclade} Downloads
Snp Sites ⭐ 173
Finds SNP sites from a multi-FASTA alignment file
most recent commit 3 years ago
Ngless ⭐ 141
NGLess: NGS with less work
total releases 5most recent commit a year ago
Ariba ⭐ 135
Antimicrobial Resistance Identification By Assembly
dependent packages 1total releases 54most recent commit a year agopypi ariba} Downloads
Gubbins ⭐ 133
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
most recent commit 5 months ago
Sarek ⭐ 126
Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing
most recent commit 4 years ago
Fqtools ⭐ 105
An efficient FASTQ manipulation suite
most recent commit 4 years ago
Rvtests ⭐ 95
Rare variant test software for next generation sequencing data
most recent commit 3 years ago
Snpgenie ⭐ 94
Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data
most recent commit 8 months ago
Assembly Stats ⭐ 92
Get assembly statistics from FASTA and FASTQ files
most recent commit a year ago
Ngseasy ⭐ 76
Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)
most recent commit 7 years ago
Czid Web ⭐ 75
Infectious Disease Sequencing Platform
most recent commit 3 months ago
Atacseq ⭐ 64
Analysis Workflow for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq)
most recent commit 8 months ago
Msisensor Pro ⭐ 63
Microsatellite Instability (MSI) detection using high-throughput sequencing data.
most recent commit 2 years ago
Deepmicrobes ⭐ 61
DeepMicrobes: taxonomic classification for metagenomics with deep learning
most recent commit 2 years ago
The 4 Most Depended On Next Generation Sequencing Open Source Projects
Seqminer ⭐ 28
Query sequence data (VCF/BCF1/BCF2, Tabix, BGEN, PLINK) in R
dependent packages 8total releases 39latest release September 02, 2023most recent commit 5 months ago
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
Nextclade ⭐ 190
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
dependent packages 2total releases 52latest release April 27, 2022most recent commit 3 months agonpm @neherlab/nextclade} 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 Next Generation Sequencing Open Source Projects
Sigalign ⭐ 10
A Similarity-Guided Alignment Algorithm
total releases 7latest release November 10, 2023most recent commit 3 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
Seqminer ⭐ 28
Query sequence data (VCF/BCF1/BCF2, Tabix, BGEN, PLINK) in R
dependent packages 8total releases 39latest release September 02, 2023most recent commit 5 months ago
Cloops2 ⭐ 32
Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.
total releases 6latest release July 20, 2023most recent commit 6 months ago
Ngless ⭐ 141
NGLess: NGS with less work
total releases 5latest release September 19, 2022most recent commit a year ago
Nextclade ⭐ 190
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
dependent packages 2total releases 52latest release April 27, 2022most recent commit 3 months agonpm @neherlab/nextclade} Downloads
Oliver ⭐ 36
An opinionated Cromwell orchestration manager.
total releases 27latest release November 20, 2021most recent commit a year ago
Wdldoc ⭐ 26
Create WDL documentation using Markdown.
total releases 14latest release September 10, 2021most recent commit a year ago
Mspc ⭐ 18
Using combined evidence from replicates to evaluate ChIP-seq peaks
total releases 14latest release March 19, 2021most recent commit 3 months ago
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