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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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  • person_outline David Jaff

Publication for DISCOVAR

DISCOVAR citations

 (26)
library_books

Chitinase genes (CHIAs) provide genomic footprints of a post Cretaceous dietary radiation in placental mammals

2018
Sci Adv
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 […]

library_books

Evolutionary instability of CUG Leu in the genetic code of budding yeasts

2018
Nat Commun
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 […]

library_books

Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis Associated Genes

2018
Genes
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 […]

library_books

The Draft Genome of the Invasive Walking Stick, Medauroidea extradendata, Reveals Extensive Lineage Specific Gene Family Expansions of Cell Wall Degrading Enzymes in Phasmatodea

2018
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 […]

library_books

The genomic and functional landscapes of developmental plasticity in the American cockroach

2018
Nat Commun
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 […]

library_books

The Most Developmentally Truncated Fishes Show Extensive Hox Gene Loss and Miniaturized Genomes

2018
Genome Biol Evol
PMCID: 5906920
PMID: 29684203
DOI: 10.1093/gbe/evy058

[…] of ∼550 bp. both paedocypris genomes were initially assembled using two different assembly programs, the “overlap-layout-consensus” based celera assembler () and the “de bruijn graph” based discovar de novo (). these two initial assemblies were then merged using metassembler software (), resulting in a reconsolidated single assembly with superior quality for each of the two paedocypris […]


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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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