Pinned Repositories
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
samclip
Filter SAM file for soft and hard clipped alignments
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
tseemann's Repositories
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/any2fasta
Convert various sequence formats to FASTA
tseemann/snp-dists
Pairwise SNP distance matrix from a FASTA sequence alignment
tseemann/samclip
Filter SAM file for soft and hard clipped alignments
tseemann/VelvetOptimiser
:chart_with_upwards_trend: Automatically optimise three of Velvet's assembly parameters.
tseemann/cgmlst-dists
🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
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/polisha
Fix small assembly errors using Illumina reads
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/bioconda-recipes
Conda recipes for the bioconda channel.
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