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The Top 21 Research Sequencing Open Source Projects

Open source projects categorized as Research Sequencing
Categories > Science > Sequencing
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
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
Assembly Stats ⭐ 92
Get assembly statistics from FASTA and FASTQ files
most recent commit a year ago
Czid Web ⭐ 75
Infectious Disease Sequencing Platform
most recent commit 3 months ago
Fastaq ⭐ 45
Python3 scripts to manipulate FASTA and FASTQ files
dependent packages 7total releases 21most recent commit 2 years agopypi pyfastaq} Downloads
Assembly_improvement ⭐ 39
Improve the quality of a denovo assembly by scaffolding and gap filling
most recent commit 4 years ago
Pathogen Informatics Training ⭐ 38
most recent commit 3 years ago
Iva ⭐ 37
de novo virus assembler of Illumina paired reads
total releases 16most recent commit 3 years ago
Gff3toembl ⭐ 20
Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
most recent commit 5 years ago
Plasmidtron ⭐ 16
Assembling the cause of phenotypes and genotypes from NGS data
most recent commit 4 years ago
Bio Tradis ⭐ 15
A set of tools to analyse the output from TraDIS analyses
total releases 14most recent commit 8 months ago
Saffrontree ⭐ 14
SaffronTree: Reference free rapid phylogenetic tree construction from raw read data
most recent commit 4 years ago
Mlst_check ⭐ 14
Multilocus sequence typing by blast using the schemes from PubMLST
total releases 13most recent commit 3 years ago
Seroba ⭐ 14
k-mer based Pipeline to identify the Serotype from Illumina NGS reads
total releases 3most recent commit 9 months ago
Seave ⭐ 12
Seave is a web platform that enables genetic variants to be easily filtered and annotated with in silico pathogenicity prediction scores and annotations from popular disease databases. Seave stores genomic variation of all types and sizes, and allows filtering for specific inheritance patterns, quality values, allele frequencies and gene lists. Seave is open source and deployable locally, or on a cloud computing provider, and works readily with gene panel, exome and whole genome data, scaling fr
most recent commit 6 years ago
Albatradis ⭐ 7
Comparative TraDIS analysis
total releases 2most recent commit a year ago
The 3 Most Depended On Research Sequencing Open Source Projects
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 Research Sequencing Open Source Projects
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
Bio Tradis ⭐ 15
A set of tools to analyse the output from TraDIS analyses
total releases 14latest release December 04, 2019most recent commit 8 months ago
Albatradis ⭐ 7
Comparative TraDIS analysis
total releases 2latest release December 03, 2019most recent commit a year ago
Roary ⭐ 219
Rapid large-scale prokaryote pan genome analysis
total releases 83latest release November 06, 2019most recent commit 2 years 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
Circlator ⭐ 193
A tool to circularize genome assemblies
total releases 33latest release January 31, 2018most recent commit 8 months ago
Iva ⭐ 37
de novo virus assembler of Illumina paired reads
total releases 16latest release January 25, 2018most recent commit 3 years ago
Seroba ⭐ 14
k-mer based Pipeline to identify the Serotype from Illumina NGS reads
total releases 3latest release November 21, 2017most recent commit 9 months ago
Mlst_check ⭐ 14
Multilocus sequence typing by blast using the schemes from PubMLST
total releases 13latest release March 03, 2017most recent commit 3 years ago
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