Torsten Seemann

prokka. :zap: :aquarius: Rapid prokaryotic genome annotation

snippy. :scissors: :zap: Rapid haploid variant calling and core genome alignment

abricate. :mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes

barrnap. :microscope: :leo: Microbial RNA annotation

mlst. :id: Scan contig files against PubMLST typing schemes

shovill. ⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads

snp-dists. Pairwise SNP distance matrix from a FASTA sequence alignment

any2fasta. Convert various sequence formats to FASTA

nullarbor. :floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology

samclip. Filter SAM file for soft and hard clipped alignments

VelvetOptimiser. :chart_with_upwards_trend: Automatically optimise three of Velvet's assembly parameters.

PEAR. Pair-End AssembeR

phastaf. Identify phage regions in bacterial genomes for masking purposes

cgmlst-dists. 🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables

seeka. Get microbial sequence data easier and faster

berokka. 🍊 💫 Trim, circularise and orient long read bacterial genome assemblies

homebrew-bioinformatics-linux. :beer: :penguin: Homebrew formulae for bioinformatics software only available for Linux

sixess. 🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files

ekidna. Assembly based core genome SNP alignments for bacteria

scripts. Miscellaneous Perl scripts from 20 years in microbial bioinformatics

scapper. Whole genome core alignments from multiple draft genomes

legsta. 🍗⭐ In silico Legionella pneumophila Sequence Based Typing

kounta. 🧮 🔢 Generate multi-sample k-mer count matrix from WGS

mokka. Annotate your metagenome assemblies

tseemann.github.io. Torsten Seemann's Home Page

snasm. Assembly based core SNP alignments

noary. 🍣 🦐 A lightweight nucleotide bacterial ortholog clustering tool

wombac. :bangbang: Rapid core genome SNP alignments from multiple bacterial genomes

trencha. Normalize VCF depth for Illumina GC bias

klosham. Find closest aligned sequences to a query sequnece

kopynumba. Identify copy number variation in bacterial Illumina sequences

spekki. Species prediction from NGS reads

injecta. Insert genes into genomes to aid synthetic test data generation

polyfix. 🔪⛓️ Repair nanopore assemblies using related genome(s)

skrofula. Yet another M.tuberculosis typing and resistance tool, but for the impatient (not in-patient)

fasterqc. A non-Java alternative to the classic FastQC tool

varion.

ragnarokka. Annotate and correct erro-prone ONT genomes

bowkaster. cgMLST from FASTQ reads

kurra. Fast whole genome phylogeny

polisha. Fix small assembly errors using Illumina reads

babykraken. 👶🦑 Very small Kraken2 database for bundling with pipelines

dehomopolymerate. Collapse sequence homopolymers to a single character

heterik. Estimate heterozygosity or mixture level of a bacterial WGS sample

perl-biotool. 🐫 🐪 Small pure Perl5 libraries for writing command line bioinformatics tools

anthrakks. Distinguish Bacillus cereus and biovar anthracis (anthrax)

bioinfo-scripts. Collection of bioinformatics utility scripts, mostly written in Bioperl

gbk2bcfgff. Convert Genbank to GFF compatible with "bcftools csq"

mini-outbreak. Small WGS dataset for testing bacterial outbreak analysis pipelines

snippa. Experimental modular bacterial SNP calling pipeline

easy-web-blast.

kroucha. Mock repository for Sanger publications citing Croucher et al