tseemann

abricate

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

any2fasta

Convert various sequence formats to FASTA

barrnap

:microscope: :leo: Bacterial ribosomal RNA predictor

mlst

:id: Scan contig files against PubMLST typing schemes

nullarbor

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

prokka

:zap: :aquarius: Rapid prokaryotic genome annotation

shovill

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

snippy

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

snp-dists

Pairwise SNP distance matrix from a FASTA sequence alignment

VelvetOptimiser

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

tseemann/prokka

:zap: :aquarius: Rapid prokaryotic genome annotation

tseemann/snippy

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

tseemann/abricate

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

tseemann/barrnap

:microscope: :leo: Bacterial ribosomal RNA predictor

tseemann/shovill

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

tseemann/mlst

:id: Scan contig files against PubMLST typing schemes

tseemann/nullarbor

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

tseemann/snp-dists

Pairwise SNP distance matrix from a FASTA sequence alignment

tseemann/any2fasta

Convert various sequence formats to FASTA

tseemann/VelvetOptimiser

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

tseemann/samclip

Filter SAM file for soft and hard clipped alignments

tseemann/cgmlst-dists

🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables

tseemann/scripts

Miscellaneous Perl scripts from 20 years in microbial bioinformatics

tseemann/tseemann.github.io

Torsten Seemann's Home Page

tseemann/legsta

🍗⭐ In silico Legionella pneumophila Sequence Based Typing

tseemann/snasm

Assembly based core SNP alignments

tseemann/wombac

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

tseemann/klosham

Find closest aligned sequences to a query sequnece

tseemann/kopynumba

Identify copy number variation in bacterial Illumina sequences

tseemann/ragnarokka

Annotate and correct erro-prone ONT genomes

tseemann/snp-sites

Finds SNP sites from a multi-FASTA alignment file

tseemann/varion

tseemann/heterik

Estimate heterozygosity or mixture level of a bacterial WGS sample

tseemann/kurra

Fast whole genome phylogeny

tseemann/anthrakks

Distinguish Bacillus cereus and biovar anthracis (anthrax)

tseemann/gbk2bcfgff

Convert Genbank to GFF compatible with "bcftools csq"

tseemann/vikka

Viral genomics toolkit for pandemics

tseemann/govaluate

Arbitrary expression evaluation for golang

tseemann/homebrew-bio

:beer::microscope: Bioinformatics formulae for the Homebrew and Linuxbrew package managers

tseemann/iupak

Decode and display IUPAC code information