VAAL statistics

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Citations per year

Number of citations per year for the bioinformatics software tool VAAL
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Tool usage distribution map

This map represents all the scientific publications referring to VAAL per scientific context
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Protocols

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

Versioning


No version available

Publication for VAAL

VAAL citations

 (14)
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Canada Wide Epidemic of emm74 Group A Streptococcus Invasive Disease

2018
PMCID: 5952926
PMID: 29780850
DOI: 10.1093/ofid/ofy085
call_split See protocol

[…] 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 wit […]

library_books

Whole genome sequencing of mutants with increased resistance against the two peptide bacteriocin plantaricin JK reveals a putative receptor and potential docking site

2017
PLoS One
PMCID: 5607208
PMID: 28931059
DOI: 10.1371/journal.pone.0185279

[…] y Blood & 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. plan […]

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Evaluation of Trace Element and Metal Accumulation and Edibility Risk Associated with Consumption of Labeo umbratus from the Vaal Dam, South Africa

2017
PMCID: 5551116
PMID: 28644416
DOI: 10.3390/ijerph14070678
call_split See protocol

[…] Heath et al. [] which have provided limits of trace elements and metals in fish tissues in wet weight levels. As there is no data available on the amount of fish consumed by people living around the Vaal Dam and in South Africa in general, the parameters used for calculation of the target hazard quotient (THQ) for each element were done according to the prescribed values suggested by the US EPA [ […]

library_books

Capsular Switching and Other Large Scale Recombination Events in Invasive Sequence Type 1 Group B Streptococcus

2016
PMCID: 5088006
PMID: 27767925
DOI: 10.3201//eid2211.152064

[…] ns 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 between str […]

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Genomic Recombination Leading to Decreased Virulence of Group B Streptococcus in a Mouse Model of Adult Invasive Disease

2016
PMCID: 5039434
PMID: 27527222
DOI: 10.3390/pathogens5030054
call_split See protocol

[…] 0). 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 […]

library_books

Fluoroquinolone Resistance among Clonal Complex 1 Group B Streptococcus Strains

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

[…] ain 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 for all 19 […]


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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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