DISCOVAR pipeline

DISCOVAR specifications

Information


Unique identifier OMICS_11253
Name DISCOVAR
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data All that is required are paired end reads, contained within one or more BAM files. For variant calling you must also supply a reference for your genome in FASTA format.
Biological technology Illumina
Operating system Unix/Linux
License Commercial
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline David Jaff <>

Publication for DISCOVAR

DISCOVAR IN pipelines

 (3)
2016
PMCID: 4833424
PMID: 26975196
DOI: 10.1093/dnares/dsw006

[…] than 499 bp were excluded., contigs or scaffolds shorter than 499 bp were excluded., for z. matrella ‘wakaba’ and z. pacifica ‘zanpa’, the scaffolds were built by opera using contigs generated by discovar de novo because discovar de novo constructed contigs with higher n50 values than the other assemblers. this may be because only a single mp library was generated for these species. the final […]

2016
PMCID: 4833424
PMID: 26975196
DOI: 10.1093/dnares/dsw006

[…] contigs or scaffolds shorter than 499 bp were excluded., for z. matrella ‘wakaba’ and z. pacifica ‘zanpa’, the scaffolds were built by opera using contigs generated by discovar de novo because discovar de novo constructed contigs with higher n50 values than the other assemblers. this may be because only a single mp library was generated for these species. the final assemblies for ‘wakaba’ […]

2016
PMCID: 5010666
PMID: 27590916
DOI: 10.1186/s12864-016-3045-z

[…] of low-complexity, segmental duplications and structural variations [36]. in addition, three other call sets were generated by gatk haplotypecaller and two de novo assembly-based callers, cortex and discovar, from 250-base paired sequencing of a pcr-free genomic library [38]. they focused more on difficult variants in regions of low-complexity and segmental duplications. the union of these four […]

DISCOVAR institution(s)
The Broad Institute of MIT and Harvard, Cambridge, MA, USA
DISCOVAR funding source(s)
This project has been funded in part with Federal funds from the National Human Genome Research Institute, National Institutes of Health, Department of Health and Human Services, under grants R01HG003474 and U54HG003067, and in part with Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract No. HHSN272200900018C.

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