VAAL protocols

VAAL statistics

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VAAL specifications

Information


Unique identifier OMICS_02170
Name VAAL
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Short reads from a ‘sample genome’ and a known sequence for a related ‘reference genome
Operating system Unix/Linux
Computer skills Advanced
Stability No
Source code URL ftp://ftp.broadinstitute.org/pub/crd/VAAL/latest_source_code/LATEST_VERSION.tar.gz
Maintained No

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Publication for VAAL

VAAL in pipelines

 (3)
2018
PMCID: 5952926
PMID: 29780850
DOI: 10.1093/ofid/ofy085

[…] for de novo assembly of illumina-generated sequences []. single nucleotide polymorphisms (snps) and short insertions/deletions (indels) were identified relative to the genome of strain ngas979 using vaal [] and/or nucmer []. whole-genome and/or core genome snps were used to construct neighbor-joining phylogenetic trees (1000 bootstrap replications) using splitstree4 []. contigs were annotated […]

2016
PMCID: 4985602
PMID: 27150273
DOI: 10.1002/mbo3.363

[…] assembly program used on flash‐merged reads gave the lowest number of contigs (243), and this assembly was the only one that gave a reasonably low number of polymorphic sites in the subsequent vaal analysis. thus, this 243‐contig assembly was used for further analyses. the contigs added up to a total of 1.59 mbp. a 34 contig assembly of the genome of a different w. viridescens strain, dms […]

2012
PMCID: 3253072
PMID: 22238576
DOI: 10.1371/journal.pone.0028316

[…] to high coverage (≥100 fold) with 76 nucleotide reads produced on the illumina platform. the reads were used to call snps against the parent assemblies using the variant ascertainment algorithm (vaal), a polymorphism discovery algorithm for short reads developed by the broad institute . select snps were confirmed independently using pcr sequencing. phylogenetic analysis was performed using […]


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VAAL in publications

 (13)
PMCID: 5607208
PMID: 28931059
DOI: 10.1371/journal.pone.0185279

[…] & tissue kit (qiagen nv, the netherlands). the genomes were sequenced using an illumina miseq instrument at the norwegian sequencing center and evaluated using the polymorphism detection tool vaal [] as previously described by oppegård et al. []. in the evaluation, we used a previously described genome assembly of w. viridescens consisting of 243 contigs []. a crude assembly of the l. […]

PMCID: 5088006
PMID: 27767925
DOI: 10.3201//eid2211.152064

[…] identified the cps locus expected for the serotype identified by latex agglutination. to characterize recombination leading to capsular switching, we first used the variant ascertainment algorithm vaal () to identify polymorphisms in each strain relative to the genome of serotype v st1 strain ss1 (genbank accession no. cp010867). the number of polymorphisms identified varied greatly […]

PMCID: 5039434
PMID: 27527222
DOI: 10.3390/pathogens5030054

[…] identification of trna-encoding regions and annotation were performed with prokka []. ortholog analysis was performed using pgap []. polymorphisms relative to strain ngbs375 were identified using vaal [] for strains for which illumina data was available, otherwise with mauve []. recombination analysis was performed using bratnextgen [] run with 20 iterations and 100 replicates, with a p-value […]

PMCID: 4983356
PMID: 27559344
DOI: 10.1155/2016/6403928

[…] ngbs061 for st459 isolates and strain sgbs001 for st1 isolates, genbank accession numbers cp007631.2 and cp010867.2, resp.) and identified polymorphisms using the variant ascertainment algorithm (vaal) []. we also investigated the presence of genes encoding putative efflux pumps which might mediate fluoroquinolone resistance. to this end, we first generated de novo genome assemblies […]

PMCID: 4985602
PMID: 27150273
DOI: 10.1002/mbo3.363

[…] program in geneious (geneious version 7 created by biomatters, available from http://www.geneious.com)). the raw assemblies were then used as reference genomes in the polymorphism detection software vaal (nusbaum et al. )., illumina reads were compared with the wild‐type genome contigs using the polymorphism discovery tool vaal., contigs harboring differences reported by vaal were annotated […]


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VAAL institution(s)
Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA; Department of Science and Technology / National Research Foundation Centre of Excellence in Biomedical Tuberculosis Research / Medical Research Council Centre for Molecular and Cellular Biology, Department of Biomedical Science, Stellenbosch University, Stellenbosch, South Africa; Department of Molecular Biology and Molecular Genetics, Harvard Medical School, Boston, MA, USA; Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Systems Biology, Harvard Medical School, Boston, MA, USA
VAAL funding source(s)
This work was supported by the National Human Genome Research Institute.

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