1. Directory
  2. Genomics
  3. Genome annotation
  4. Repetitive DNA
Join community Sign in
By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.

A variant caller and small genome assembler. The heart of DISCOVAR is a de novo genome assembler, one that is accurate enough to produce assemblies that can be used for variant calling given a reference sequence. DISCOVAR can also generate de novo assemblies for small genomes, but consider using DISCOVAR de novo instead which can assemble genomes up to mammalian size. DISCOVAR provides a more complete inventory of an individual’s genetic variants than had been previously possible. As such, it adds to the tools that can be used to probe the genetic basis of disease. It may be particularly useful in cases where targeted or exome sequencing fails to find causal mutations.

Software type:
Package
Interface:
Command line interface
Restrictions to use:
Academic users only
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.
Operating system:
Unix/Linux
License:
Commercial
Computer skills:
Advanced
Stability:
Stable
View all reviews

0 user review

No review has been posted.

View all issues

0 issue

No open issue.

Links

Institution(s)

The Broad Institute of MIT and Harvard, Cambridge, MA, USA

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.

  • (Weisenfeld et al., 2014) Comprehensive variation discovery in single human genomes. Nature genetics.
    PMID: 25326702
  • (Mainzer et al., 2015) Isaac, the Illumina variant calling workflow. bioRxiv.
    DOI: 10.1101/031021
  • (Liu et al., 2013) Variant callers for next-generation sequencing data: a comparison study. PloS one.
    PMID: 24086590
  • (Nielsen et al., 2011) Genotype and SNP calling from next-generation sequencing data. Nature reviews Genetics.
    PMID: 21587300
  • (Altmann et al., 2012) A beginners guide to SNP calling from high-throughput DNA-sequencing data. Human genetics.
    PMID: 22886560
  • (Pabinger et al., 2013) A survey of tools for variant analysis of next-generation genome sequencing data. Briefings in bioinformatics.
    PMID: 23341494
  • (Yi et al., 2014) Performance comparison of SNP detection tools with illumina exome sequencing data-an assessment using both family pedigree information and sample-matched SNP array data. Nucleic acids research.
    PMID: 24831545
  • (Pirooznia et al., 2014) Validation and assessment of variant calling pipelines for next-generation sequencing. Human genomics.
    PMID: 25078893

77 related tools