LAVA specifications

Information


Unique identifier OMICS_12714
Name LAVA
Alternative name Lightweight Assignment of Variant Alleles
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A reference genome, a list of SNPs, and a set of reads.
Input format FASTA, UCSC's txt
Output data Some predicted genotypes for those SNPs (wild-type, heterozygous, homozygous mutant).
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Requirements
GCC, make
Maintained Yes

Download


download.png
github.png

Versioning


No version available

Documentation


Maintainer


  • person_outline Bonnie Berger

Publication for Lightweight Assignment of Variant Alleles

LAVA citation

library_books

Alignment free sequence comparison: benefits, applications, and tools

2017
Genome Biol
PMCID: 5627421
PMID: 28974235
DOI: 10.1186/s13059-017-1319-7

[…] lymorphisms. These genomic alterations are typically detected by genotype calling on mapped reads (e.g., Samtools mpileup [] and GATK HaplotypeCaller []). However, alignment-free tools (FastGT [] and LAVA []) allow for genotyping of known variants directly from next-generation sequencing data, based on k-mer analysis. Since these methods are 1–2 orders of magnitude faster than traditional mapping- […]

LAVA institution(s)
Department of Electrical & Computer Engineering, Boston University, Boston, MA, USA; Computer Science and AI Lab, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA
LAVA funding source(s)
Supported by the National Institutes of Health (NIH) R01GM108348; the Fannie and John Hertz Foundation; HHMI; and IBM.

LAVA reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review LAVA