DISCOVAR protocols

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DISCOVAR specifications


Unique identifier OMICS_11253
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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  • person_outline David Jaff <>

Publication for DISCOVAR

DISCOVAR in pipelines

PMCID: 4779211
PMID: 26944054
DOI: 10.1186/s12864-016-2531-7

[…] walker [, ]. variant positions were extracted and used to calculate variant density by contig. contigs not present in the variant list were assumed to be homozygous., one of the outputs of discovar de novo is a file representing genome polymorphism in a fasta format enriched with “bubbles,” or forks in the de bruijn graph. each bubble contains the alleles predicted in the sequencing […]

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 […]

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

[…] of low-complexity, segmental duplications and structural variations []. 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 []. they focused more on difficult variants in regions of low-complexity and segmental duplications. the union of these four […]

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DISCOVAR in publications

PMCID: 5955627
PMID: 29774238
DOI: 10.1126/sciadv.aar6478

[…] examined were available in national center for biotechnology information (ncbi)’s nucleotide collection and whole-genome shotgun (wgs) contig database except three assemblies generated using the discovar de novo protocol (tamandua tetradactyla, chaetophractus vellerosus, and tolypeutes matacus; https://software.broadinstitute.org/software/discovar/blog/) and made available to us by the broad […]

PMCID: 5951914
PMID: 29760453
DOI: 10.1038/s41467-018-04374-7

[…] the assembly with the highest n50: the leu2 clade species saturnispora dispora (strain nrrl y-1447, spades assembly), ambrosiozyma philentoma (nrrl y-7523, spades), candida boidinii (nrrl y-2332, discovar), and citeromyces matritensis (nrrl y-2407, masurca); the ala clade species nakazawaea wickerhamii (nrrl y-2563, discovar) and peterozyma xylosa (nrrl y-12939, discovar); and the ser2 clade […]

PMCID: 5924527
PMID: 29597328
DOI: 10.3390/genes9040185

[…] artificial chromosome (bac) end library. read length and actual insert sizes for each library are given in (). this sequencing scheme was specially developed for the initial contig assembly by the discovar assembler [], followed by scaffolding. construction of genomic libraries and sequencing were performed following lee et al []., filtration of the pe library lib400 was performed in two […]

PMCID: 5940134
PMID: 29588379
DOI: 10.1534/g3.118.200204

[…] many parts of the world. the ease of culturing these insects in the lab, and their widespread distribution, makes them a suitable potential model system for laboratory studies of pcwdes. we used the discovar approach coupled with rna-seq based scaffolding to produce the draft genome. annotation of the genome, assisted by several rna-seq datasets, produced a high-quality gene set comparable […]

PMCID: 5861062
PMID: 29559629
DOI: 10.1038/s41467-018-03281-1

[…] for the messenger rna pool of all stages of cockroach development (supplementary table )., initial assemblies were generated by discovardenovo (v52488; https://software.broadinstitute.org/software/discovar/blog/) with default settings. sspace (v3) was then used to join contigs into scaffolds based on linking evidence of mate pair libraries, step by step ranging from 600 bp to 13 kb insert […]

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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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