This is your work, valued

Melbourne, AUSTRALIA

Torsten Seemann

Elite
@tseemann

Bioinformatics and genomics for public health and clinical microbiology

tseemann.github.io/

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

993

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

594

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

502

barrnap. :microscope: :leo: Microbial RNA annotation

306

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

295

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

261

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

156

any2fasta. Convert various sequence formats to FASTA

148

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

144

samclip. Filter SAM file for soft and hard clipped alignments

53

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

50

PEAR. Pair-End AssembeR

35

phastaf. Identify phage regions in bacterial genomes for masking purposes

33

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

29

seeka. Get microbial sequence data easier and faster

29

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

28

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

27

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

25

ekidna. Assembly based core genome SNP alignments for bacteria

25

scripts. Miscellaneous Perl scripts from 20 years in microbial bioinformatics

18

scapper. Whole genome core alignments from multiple draft genomes

13

legsta. 🍗⭐ In silico Legionella pneumophila Sequence Based Typing

12

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

11

mokka. Annotate your metagenome assemblies

11

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

9

snasm. Assembly based core SNP alignments

8

noary. 🍣 🦐 A lightweight nucleotide bacterial ortholog clustering tool

7

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

7

trencha. Normalize VCF depth for Illumina GC bias

7

klosham. Find closest aligned sequences to a query sequnece

6

kopynumba. Identify copy number variation in bacterial Illumina sequences

6

spekki. Species prediction from NGS reads

5

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

5

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

5

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

5

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

5

varion.

5

ragnarokka. Annotate and correct erro-prone ONT genomes

4

bowkaster. cgMLST from FASTQ reads

4

kurra. Fast whole genome phylogeny

4

polisha. Fix small assembly errors using Illumina reads

4

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

4

dehomopolymerate. Collapse sequence homopolymers to a single character

4

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

3

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

3

anthrakks. Distinguish Bacillus cereus and biovar anthracis (anthrax)

3

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

3

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

2

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

2

snippa. Experimental modular bacterial SNP calling pipeline

2

easy-web-blast.

2

kroucha. Mock repository for Sanger publications citing Croucher et al

1