tseemann/prokka

:zap: :aquarius: Rapid prokaryotic genome annotation

Language: Perl - Size: 314 MB - Last synced: 13 days ago - Pushed: about 1 month ago - Stars: 759 - Forks: 217

tseemann/abricate

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

Language: Perl - Size: 15.5 MB - Last synced: 30 days ago - Pushed: 5 months ago - Stars: 329 - Forks: 85

tseemann/nullarbor

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

Language: Perl - Size: 11.3 MB - Last synced: 7 months ago - Pushed: almost 4 years ago - Stars: 123 - Forks: 35

tseemann/wombac

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

Language: Perl - Size: 6.8 MB - Last synced: 7 months ago - Pushed: about 1 year ago - Stars: 7 - Forks: 1

tseemann/VelvetOptimiser

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

Language: Perl - Size: 5.57 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 45 - Forks: 18

tseemann/sixess

🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files

Language: Shell - Size: 36.9 MB - Last synced: 4 months ago - Pushed: about 6 years ago - Stars: 23 - Forks: 2

tseemann/snp-dists

Pairwise SNP distance matrix from a FASTA sequence alignment

Language: C - Size: 52.7 KB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 100 - Forks: 27

tseemann/mlst

:id: Scan contig files against PubMLST typing schemes

Language: Shell - Size: 147 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 165 - Forks: 40

tseemann/barrnap

:microscope: :leo: Bacterial ribosomal RNA predictor

Language: Perl - Size: 13.3 MB - Last synced: 7 months ago - Pushed: 8 months ago - Stars: 184 - Forks: 41

tseemann/cgmlst-dists

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

Language: C - Size: 237 KB - Last synced: 7 months ago - Pushed: 8 months ago - Stars: 21 - Forks: 6

tseemann/snippy

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

Language: Perl - Size: 124 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 408 - Forks: 111

tseemann/phastaf

Identify phage regions in bacterial genomes for masking purposes

Language: Perl - Size: 18.4 MB - Last synced: 7 months ago - Pushed: over 4 years ago - Stars: 28 - Forks: 4

tseemann/berokka

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

Language: Perl - Size: 3.51 MB - Last synced: 7 months ago - Pushed: over 4 years ago - Stars: 24 - Forks: 4

tseemann/ekidna

Assembly based core genome SNP alignments for bacteria

Language: Perl - Size: 4.1 MB - Last synced: 7 months ago - Pushed: over 4 years ago - Stars: 24 - Forks: 3

tseemann/bng-tools

Useful post-processing scripts for BRATNextGen output data

Language: Perl - Size: 172 KB - Last synced: 7 months ago - Pushed: almost 10 years ago - Stars: 0 - Forks: 0

tseemann/any2fasta

Convert various sequence formats to FASTA

Language: Perl - Size: 6.24 MB - Last synced: 7 months ago - Pushed: almost 2 years ago - Stars: 106 - Forks: 14

tseemann/shovill

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

Language: Perl - Size: 11.9 MB - Last synced: 7 months ago - Pushed: about 1 year ago - Stars: 185 - Forks: 38

tseemann/samclip

Filter SAM file for soft and hard clipped alignments

Language: Perl - Size: 43.9 KB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 44 - Forks: 9

tseemann/homebrew-bioinformatics-linux

:beer: :penguin: Homebrew formulae for bioinformatics software only available for Linux

Language: Ruby - Size: 93.8 KB - Last synced: 20 days ago - Pushed: over 4 years ago - Stars: 27 - Forks: 7

tseemann/legsta

🍗⭐ In silico Legionella pneumophila Sequence Based Typing

Language: Perl - Size: 6.97 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 7 - Forks: 3

tseemann/PEAR

Pair-End AssembeR

Language: C - Size: 37.7 MB - Last synced: 7 months ago - Pushed: about 10 years ago - Stars: 20 - Forks: 38

tseemann/scapper

Whole genome core alignments from multiple draft genomes

Language: Perl - Size: 22.5 KB - Last synced: about 1 year ago - Pushed: over 7 years ago - Stars: 8 - Forks: 4

tseemann/snp-sites Fork of sanger-pathogens/snp-sites

Finds SNP sites from a multi-FASTA alignment file

Language: C - Size: 14.7 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 2 - Forks: 0

tseemann/noary

🍣 🦐 A lightweight nucleotide bacterial ortholog clustering tool

Language: Perl - Size: 23.4 KB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 6 - Forks: 2

tseemann/seeka

Get microbial sequence data easier and faster

Language: Perl - Size: 40 KB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 27 - Forks: 4

tseemann/kounta

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

Language: Perl - Size: 93.8 KB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 8 - Forks: 3

tseemann/varion

Size: 15.6 KB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 5 - Forks: 0

tseemann/perl-biotool

🐫 🐪 Small pure Perl5 libraries for writing command line bioinformatics tools

Language: Perl - Size: 131 KB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 3 - Forks: 0

tseemann/ClonalFrameML Fork of xavierdidelot/ClonalFrameML

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

Language: C++ - Size: 303 KB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 2 - Forks: 0

tseemann/Roary Fork of sanger-pathogens/Roary

Rapid large-scale prokaryote pan genome analysis

Size: 17.7 MB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 2 - Forks: 1

tseemann/klosham

Find closest aligned sequences to a query sequnece

Language: C - Size: 21.5 KB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 6 - Forks: 0

tseemann/bioinfo-scripts

Collection of bioinformatics utility scripts, mostly written in Bioperl

Language: Perl - Size: 2.57 MB - Last synced: about 1 year ago - Pushed: almost 7 years ago - Stars: 2 - Forks: 2

tseemann/spekki

Species prediction from NGS reads

Language: Python - Size: 16.6 KB - Last synced: about 1 year ago - Pushed: over 6 years ago - Stars: 4 - Forks: 1

tseemann/babykraken

👶🦑 Very small Kraken2 database for bundling with pipelines

Size: 14.6 KB - Last synced: about 1 year ago - Pushed: almost 5 years ago - Stars: 4 - Forks: 0

tseemann/fasterqc

A non-Java alternative to the classic FastQC tool

Language: Perl - Size: 62.5 KB - Last synced: about 1 year ago - Pushed: almost 6 years ago - Stars: 5 - Forks: 0

tseemann/tseemann.github.io

Torsten Seemann's Home Page

Language: HTML - Size: 203 KB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 6 - Forks: 0

tseemann/canu Fork of marbl/canu

A single molecule sequence assembler for genomes large and small.

Size: 194 MB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 1 - Forks: 0

tseemann/TBProfiler Fork of jodyphelan/TBProfiler

Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data

Language: Python - Size: 5.72 MB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 1 - Forks: 0

tseemann/skrilla

It ain't all about skrilla

Size: 13.7 KB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 1 - Forks: 0

tseemann/anthrakks

Distinguish Bacillus cereus and biovar anthracis (anthrax)

Size: 13.7 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 3 - Forks: 0

tseemann/joystx

Shigatoxin STX typing for E.coli STEC

Size: 13.7 KB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

tseemann/trencha

Normalize VCF depth for Illumina GC bias

Language: Perl - Size: 128 KB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 6 - Forks: 0

tseemann/easy-web-blast

Size: 156 KB - Last synced: about 1 year ago - Pushed: over 11 years ago - Stars: 2 - Forks: 1

tseemann/ragnarokka

Annotate and correct erro-prone ONT genomes

Size: 13.7 KB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 4 - Forks: 0

tseemann/iupak

Decode and display IUPAC code information

Size: 13.7 KB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

tseemann/vikka

Viral genomics toolkit for pandemics

Size: 13.7 KB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 1 - Forks: 0

tseemann/govaluate Fork of Knetic/govaluate

Arbitrary expression evaluation for golang

Size: 308 KB - Last synced: 11 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

tseemann/heterik

Estimate heterozygosity or mixture level of a bacterial WGS sample

Size: 13.7 KB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 3 - Forks: 0

tseemann/bowkaster

cgMLST from FASTQ reads

Size: 14.6 KB - Last synced: about 1 year ago - Pushed: about 6 years ago - Stars: 3 - Forks: 1

tseemann/SpartanBioinformatics Fork of UoM-ResPlat-DevOps/SpartanBioinformatics

Language: HTML - Size: 2.63 MB - Last synced: about 1 year ago - Pushed: almost 5 years ago - Stars: 1 - Forks: 0

tseemann/kurra

Fast whole genome phylogeny

Size: 13.7 KB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 4 - Forks: 0

tseemann/freebayes Fork of freebayes/freebayes

Bayesian haplotype-based polymorphism discovery and genotyping.

Language: C++ - Size: 6.84 MB - Last synced: about 1 year ago - Pushed: about 9 years ago - Stars: 0 - Forks: 0

tseemann/panito Fork of sanger-pathogens/panito

Calculate genome wide average nucleotide identity (gwANI) for a multiFASTA alignment

Language: C - Size: 109 KB - Last synced: about 1 year ago - Pushed: almost 7 years ago - Stars: 1 - Forks: 2

tseemann/polyfix

🔪⛓️ Repair nanopore assemblies using related genome(s)

Language: Perl - Size: 20.5 KB - Last synced: about 1 year ago - Pushed: almost 5 years ago - Stars: 5 - Forks: 0

tseemann/polisha

Fix small assembly errors using Illumina reads

Language: Perl - Size: 21.5 KB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 4 - Forks: 0

tseemann/gard

🍆 💊 Gonococcal Antimicrobial Resistance Detection

Size: 13.7 KB - Last synced: about 1 year ago - Pushed: about 7 years ago - Stars: 1 - Forks: 0

tseemann/coginator

Assign COGs to protein sequences

Size: 121 KB - Last synced: about 1 year ago - Pushed: about 9 years ago - Stars: 1 - Forks: 0

tseemann/assembill

Simple script to clip, assemble, tile and annotate a bacterial genome from Illumina reads

Language: Shell - Size: 145 KB - Last synced: about 1 year ago - Pushed: almost 10 years ago - Stars: 1 - Forks: 0

tseemann/vadr Fork of ncbi/vadr

Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation

Size: 33.8 MB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0

tseemann/homebrew-bio Fork of brewsci/homebrew-bio

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

Language: Ruby - Size: 1.81 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

tseemann/kopynumba

Identify copy number variation in bacterial Illumina sequences

Size: 14.6 KB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 6 - Forks: 0

tseemann/quicktree Fork of khowe/quicktree

Fast implementation of the neighbour-joining phylogenetic inference method

Language: C - Size: 93.8 KB - Last synced: about 1 year ago - Pushed: about 7 years ago - Stars: 3 - Forks: 1

tseemann/GraphAligner Fork of maickrau/GraphAligner

Size: 1.59 MB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 1 - Forks: 0

tseemann/bioconda-recipes Fork of bioconda/bioconda-recipes

Conda recipes for the bioconda channel.

Language: Shell - Size: 260 MB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

tseemann/arborkart

Phylogenomic trees with maps for the web

Size: 15.6 KB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 1 - Forks: 0

tseemann/homebrew-core Fork of Homebrew/homebrew-core

🍻 Default formulae for the missing package manager for macOS

Language: Ruby - Size: 278 MB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0

tseemann/lathe Fork of bhattlab/lathe

A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing

Size: 345 KB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 1 - Forks: 0

tseemann/artic-ncov2019 Fork of artic-network/artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus

Size: 7.81 MB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0

tseemann/skrofula

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

Language: Perl - Size: 78.9 MB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 5 - Forks: 0

tseemann/vcf2phylip Fork of edgardomortiz/vcf2phylip

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

Size: 82 KB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 1 - Forks: 1

tseemann/MapCaller Fork of hsinnan75/MapCaller

MapCaller – An efficient and versatile approach for short-read alignment and variant detection in high-throughput sequenced genomes

Language: C - Size: 1.76 MB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 0 - Forks: 1

tseemann/linuxbrew-core Fork of Homebrew/linuxbrew-core

🍻🐧 Core formulae for the Homebrew package manager on Linux

Language: Ruby - Size: 292 MB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0

tseemann/SeqSero Fork of denglab/SeqSero

Salmonella serotyping from genome sequencing data

Language: Python - Size: 758 KB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 1 - Forks: 1

tseemann/Unicycler Fork of rrwick/Unicycler

hybrid assembly pipeline for bacterial genomes

Size: 36.9 MB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 1

tseemann/mokka

Annotate your metagenome assemblies

Size: 13.7 KB - Last synced: about 1 year ago - Pushed: almost 6 years ago - Stars: 10 - Forks: 1

tseemann/spades Fork of ablab/spades

SPAdes Genome Assembler http://cab.spbu.ru/spades

Language: C++ - Size: 44.7 MB - Last synced: about 1 year ago - Pushed: almost 8 years ago - Stars: 1 - Forks: 0

tseemann/piggy Fork of harry-thorpe/piggy

Pan intergenic

Language: Perl - Size: 3.15 MB - Last synced: about 1 year ago - Pushed: almost 7 years ago - Stars: 1 - Forks: 0

tseemann/cdhit Fork of weizhongli/cdhit

Automatically exported from code.google.com/p/cdhit

Language: Perl - Size: 3.07 MB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 2 - Forks: 0

tseemann/TZMD Fork of Yizhuangzhou/TZMD

Size: 115 KB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

tseemann/mreps Fork of gregorykucherov/mreps

mreps: software for tandem repeat identification in DNA

Size: 50.8 KB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

tseemann/minimap2 Fork of lh3/minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Language: C - Size: 1.21 MB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

tseemann/kalign Fork of TimoLassmann/kalign

A fast multiple sequence alignment program.

Size: 1.17 MB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

tseemann/dehomopolymerate

Collapse sequence homopolymers to a single character

Language: C - Size: 27.3 KB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 4 - Forks: 2

tseemann/Mash Fork of marbl/Mash

Fast genome and metagenome distance estimation using MinHash

Size: 4.38 MB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

tseemann/seqtk Fork of lh3/seqtk

Toolkit for processing sequences in FASTA/Q formats

Language: C - Size: 164 KB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 1 - Forks: 0

tseemann/amplikate

📢🎯 Generic typing tool from amplicons and/or in silico PCR

Language: Perl - Size: 129 KB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 0 - Forks: 1

tseemann/PIRATE Fork of SionBayliss/PIRATE

A toolbox for pangenome analysis and threshold evaluation.

Language: Perl - Size: 5.67 MB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 2 - Forks: 2

tseemann/injecta

Insert genes into genomes to aid synthetic test data generation

Language: Perl - Size: 25.4 KB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 4 - Forks: 0

tseemann/mini-outbreak

Small WGS dataset for testing bacterial outbreak analysis pipelines

Size: 14.6 KB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 2 - Forks: 0

tseemann/homebrew-science Fork of brewsci/homebrew-science

:snowflake: Scientific formulae for Homebrew and Linuxbrew (legacy)

Language: Ruby - Size: 9.1 MB - Last synced: about 1 year ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0

tseemann/kroucha

Mock repository for Sanger publications citing Croucher et al

Size: 14.6 KB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 1 - Forks: 0

tseemann/tiptoft Fork of andrewjpage/tiptoft

Predict plasmids from uncorrected long read data

Language: Python - Size: 37.9 MB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 0 - Forks: 2

tseemann/asmngs18 Fork of asmngs/asmngs18

ASMNGS18 - 2018 Conference Details

Size: 107 KB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

tseemann/wtfq

Duplicate FASTQ reads to address undersequenced regions

Language: C - Size: 22.5 KB - Last synced: about 1 year ago - Pushed: about 6 years ago - Stars: 0 - Forks: 1

tseemann/homebrew-extra Fork of Linuxbrew/homebrew-extra

:candy::penguin: Linux-only formulae that are not dependencies of core formulae

Language: Ruby - Size: 37.1 KB - Last synced: about 1 year ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

tseemann/snippa

Experimental modular bacterial SNP calling pipeline

Language: Perl - Size: 60.5 KB - Last synced: about 1 year ago - Pushed: about 6 years ago - Stars: 1 - Forks: 1

tseemann/mlst-1 Fork of phgenomics-singularity/mlst

Singularity container for MLST

Language: Roff - Size: 7.81 KB - Last synced: about 1 year ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

tseemann/MUMmer3 Fork of marbl/MUMmer3

MUMmer3

Language: C++ - Size: 3.58 MB - Last synced: about 1 year ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0

tseemann/simuvar

Simulate variants of bacterial genomes for testing SNP callers

Size: 13.7 KB - Last synced: about 1 year ago - Pushed: almost 7 years ago - Stars: 0 - Forks: 1

tseemann/cfml-maskrc Fork of kwongj/cfml-maskrc

Masks recombinant regions in an alignment based on ClonalFrameML output

Language: Python - Size: 14.6 KB - Last synced: about 1 year ago - Pushed: about 7 years ago - Stars: 1 - Forks: 1