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prokka
โก โ Rapid prokaryotic genome annotationsnippy
โ๏ธ โก Rapid haploid variant calling and core genome alignmentabricate
๐ ๐ Mass screening of contigs for antimicrobial and virulence genesshovill
โกโ ๏ธ Assemble bacterial isolate genomes from Illumina paired-end readsbarrnap
๐ฌ โ Bacterial ribosomal RNA predictormlst
๐ Scan contig files against PubMLST typing schemesnullarbor
๐พ ๐ "Reads to report" for public health and clinical microbiologysnp-dists
Pairwise SNP distance matrix from a FASTA sequence alignmentany2fasta
Convert various sequence formats to FASTAVelvetOptimiser
๐ Automatically optimise three of Velvet's assembly parameters.samclip
Filter SAM file for soft and hard clipped alignmentsphastaf
Identify phage regions in bacterial genomes for masking purposesseeka
Get microbial sequence data easier and fasterhomebrew-bioinformatics-linux
๐บ ๐ง Homebrew formulae for bioinformatics software only available for Linuxberokka
๐ ๐ซ Trim, circularise and orient long read bacterial genome assembliesekidna
Assembly based core genome SNP alignments for bacteriasixess
๐ฌ๐ Rapid 16s rRNA identification from isolate FASTQ filescgmlst-dists
๐ปโ๐จ Calculate distance matrix from ChewBBACA cgMLST allele call tablesPEAR
Pair-End AssembeRmokka
Annotate your metagenome assembliesscapper
Whole genome core alignments from multiple draft genomeskounta
๐งฎ ๐ข Generate multi-sample k-mer count matrix from WGStrencha
Normalize VCF depth for Illumina GC biassnasm
Assembly based core SNP alignmentstseemann.github.io
Torsten Seemann's Home Pagenoary
๐ฃ ๐ฆ A lightweight nucleotide bacterial ortholog clustering toolwombac
โผ๏ธ Rapid core genome SNP alignments from multiple bacterial genomesklosham
Find closest aligned sequences to a query sequnecekopynumba
Identify copy number variation in bacterial Illumina sequencesfasterqc
A non-Java alternative to the classic FastQC toolragnarokka
Annotate and correct erro-prone ONT genomesspekki
Species prediction from NGS readspolisha
Fix small assembly errors using Illumina readspolyfix
๐ชโ๏ธ Repair nanopore assemblies using related genome(s)skrofula
Yet another M.tuberculosis typing and resistance tool, but for the impatient (not in-patient)varion
injecta
Insert genes into genomes to aid synthetic test data generationkurra
Fast whole genome phylogenyheterik
Estimate heterozygosity or mixture level of a bacterial WGS sampledehomopolymerate
Collapse sequence homopolymers to a single characterbabykraken
๐ถ๐ฆ Very small Kraken2 database for bundling with pipelinesbowkaster
cgMLST from FASTQ readsperl-biotool
๐ซ ๐ช Small pure Perl5 libraries for writing command line bioinformatics toolsanthrakks
Distinguish Bacillus cereus and biovar anthracis (anthrax)bioinfo-scripts
Collection of bioinformatics utility scripts, mostly written in Bioperlgbk2bcfgff
Convert Genbank to GFF compatible with "bcftools csq"easy-web-blast
mini-outbreak
Small WGS dataset for testing bacterial outbreak analysis pipelinessnippa
Experimental modular bacterial SNP calling pipelinevikka
Viral genomics toolkit for pandemicsgard
๐ ๐ Gonococcal Antimicrobial Resistance Detectionwtfq
Duplicate FASTQ reads to address undersequenced regionssimuvar
Simulate variants of bacterial genomes for testing SNP callerscoginator
Assign COGs to protein sequencesskrilla
It ain't all about skrillaarborkart
Phylogenomic trees with maps for the webassembill
Simple script to clip, assemble, tile and annotate a bacterial genome from Illumina readskroucha
Mock repository for Sanger publications citing Croucher et alLove Open Source and this site? Check out how you can help us