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The Top 23 Bioinformatics Pathogen Open Source Projects

Open source projects categorized as Bioinformatics Pathogen
Categories > Data Processing > Bioinformatics
Categories > Pathogen
Roary ⭐ 219
Rapid large-scale prokaryote pan genome analysis
total releases 83most recent commit 2 years ago
Amr ⭐ 203
AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
most recent commit 4 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
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
Taxprofiler ⭐ 78
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
most recent commit 3 months ago
Microbetrace ⭐ 53
The Visualization Multitool for Molecular Epidemiology and Bioinformatics
most recent commit 2 years 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
Pathogentrack ⭐ 22
A pipeline to identify pathogenic microorganisms from scRNA-seq raw data.
most recent commit 7 months ago
Gff3toembl ⭐ 20
Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
most recent commit 5 years ago
Tiptoft ⭐ 20
Predict plasmids from uncorrected long read data
total releases 6most recent commit 4 years ago
Phat ⭐ 17
Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform
most recent commit 2 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 9 months ago
Seroba ⭐ 14
k-mer based Pipeline to identify the Serotype from Illumina NGS reads
total releases 3most recent commit 9 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
The 2 Most Depended On Bioinformatics Pathogen 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
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 Bioinformatics Pathogen Open Source Projects
Ariba ⭐ 135
Antimicrobial Resistance Identification By Assembly
dependent packages 1total releases 54latest release September 07, 2020most recent commit a year agopypi ariba} Downloads
Tiptoft ⭐ 20
Predict plasmids from uncorrected long read data
total releases 6latest release December 05, 2019most recent commit 4 years ago
Bio Tradis ⭐ 15
A set of tools to analyse the output from TraDIS analyses
total releases 14latest release December 04, 2019most recent commit 9 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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