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Wombac specifications

Information


Unique identifier OMICS_13061
Name Wombac
Alternative name Wombat Bacteria
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A reference genome
Input format FASTA
Output data Wombac produces standards-compliant output files.
Output format BAM, VCF, ALN
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Requirements
Perl, Bwa mem, Samtools, Freebayes, vcflib, bgzip, tabix
Maintained Yes

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Maintainer


  • person_outline Torsten Seeman

Wombac citations

 (6)
call_split

Yersinia pestis strains of ancient phylogenetic branch 0.ANT are widely spread in the high mountain plague foci of Kyrgyzstan

2017
PLoS One
PMCID: 5658180
PMID: 29073248
DOI: 10.1371/journal.pone.0187230
call_split See protocol

[…] id, which is found in all strains of this branch.To identify the relation of Y. pestis strains to certain phylogenetic populations marker SNPs were found (). The search of the SNPs was conducted with Wombac v2.1 software (https://github.com/tseemann/wombac), based on the comparison between whole genome sequences of Y. pestis strains, representing different phylogenetic branches. For SNP typing, ea […]

library_books

Comparative genomics of Enterococcus spp. isolated from bovine feces

2017
BMC Microbiol
PMCID: 5341189
PMID: 28270110
DOI: 10.1186/s12866-017-0962-1

[…] likelihood. The resulting tree was visualized using FigTree software (http://tree.bio.ed.ac.uk/software/figtree/). When included in the analyses, complete genomes from NCBI database were run through Wombac Shred (https://github.com/tseemann/wombac/blob/master/bin/wombac-shred_fasta) or art illumina [] to generate paired-end reads with 2 × 250 bp length and >30X coverage. The resulting reads along […]

call_split

Comparative analysis of Corynebacterium glutamicum genomes: a new perspective for the industrial production of amino acids

2017
BMC Genomics
PMCID: 5310272
PMID: 28198668
DOI: 10.1186/s12864-016-3255-4
call_split See protocol

[…] ] for mapping reads, Samtools 0.1.19 [] for data interaction, and Tablet 1.14.4.10 [] for assembly/mapping visualization. SnpEff 4.1e [] was used for genetic variant annotation and effect prediction. Wombac 2.0 [] was used to finds genome single nucleotide polymorphisms (SNPs) and build a phylogenomic tree for highly related strains. Whole-genome alignments were calculated using MUMmer 3.0 []. […]

call_split

Bacillus cereus Biovar Anthracis Causing Anthrax in Sub Saharan Africa—Chromosomal Monophyly and Broad Geographic Distribution

2016
PLoS Negl Trop Dis
PMCID: 5015827
PMID: 27607836
DOI: 10.1371/journal.pntd.0004923
call_split See protocol

[…] available at github (https://github.com/apetkau/core-phylogenomics; commit version 0317413ba9). To ensure consistent data across all strains, in silico error free illumina reads were generated using Wombac from contigs available on NCBI. This was only done for strains without any publicly available raw reads http://www.vicbioinformatics.com/software.wombac.shtml (version dated Oct 3, 2013). All p […]

call_split

Comparative Genomics of Carriage and Disease Isolates of Streptococcus pneumoniae Serotype 22F Reveals Lineage Specific Divergence and Niche Adaptation

2016
Genome Biol Evol
PMCID: 4860696
PMID: 27016484
DOI: 10.1093/gbe/evw066
call_split See protocol

[…] me comparisons were undertaken using the sequence comparison tool in RAST () and BLAST Ring Image Generator (BRIG) (). Core genome single nucleotide polymorphism (SNP) phylogeny was constructed using Wombac v2.0 (https://github.com/tseemann/wombac, last accessed March 30, 2016) with resultant trees visualized using FigTree v1.4.2 (http://tree.bio.ed.ac.uk/software/figtree/, last accessed March 30, […]

library_books

Comparative Genomic Analysis of Asian Haemorrhagic Septicaemia Associated Strains of Pasteurella multocida Identifies More than 90 Haemorrhagic Septicaemia Specific Genes

2015
PLoS One
PMCID: 4495038
PMID: 26151935
DOI: 10.1371/journal.pone.0130296

[…] hylogenetic relationship between the strains was predicted by analysis of core genome single nucleotide polymorphisms (CG-SNPs). Identification of CG-SNPs and phylogenetic analysis was assessed using Wombac v1.2 (https://github.com/tseemann/wombac). The four closely related species, Gallibacterium anatis, Mannheimia haemolytica, P. bettyae and P. dagmatis were used as outgroups. The P. multocida s […]

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