WHAM specifications

Information


Unique identifier OMICS_00697
Name WHAM
Alternative name Wisconsin’s High-throughput Alignment Method
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A set of query sequences of equal length, a database of reference sequence(s), and an error model.
Operating system Unix/Linux
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

Download


conda.png

Versioning


No version available

Maintainers


  • person_outline Jignesh M. Patel
  • person_outline Yinan Li
  • person_outline Allison Terrell

Additional information


http://research.cs.wisc.edu/wham/manual/

Publication for Wisconsin’s High-throughput Alignment Method

WHAM citation

library_books

A hybrid short read mapping accelerator

2013
BMC Bioinformatics
PMCID: 3598928
PMID: 23441908
DOI: 10.1186/1471-2105-14-67

[…] res for each base. ZOOM [] uses “spaced-seeds” in order to improve sensitivity. SHRiMP [] combines the spaced seeds and the Smith-Waterman algorithm to align reads with even higher sensitivity. SOAP, WHAM, BFAST, and GASSST apply the second approach to conduct the alignment computation. SOAP [] uses seeds (consecutive bases) and a hash lookup table algorithm to accelerate the alignment and is effi […]

WHAM institution(s)
University of Wisconsin–Madison, Madison, WI, USA
WHAM funding source(s)
Supported in part by a grant from the National Science Foundation under grant DBI-0926269.

WHAM reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review WHAM