General Information
| Description | A fast algorithm for k-mismatch mapping |
| Homepage | http://code.google.com/p/batmis/ |
Publications
BatMis: a fast algorithm for k-mismatch mapping
Motivation:
Second-generation sequencing (SGS) generates millions of reads that need to be aligned to a reference genome allowing errors. Although current aligners can efficiently map reads allowing a small number of mismatches, they are not well suited for handling a large number of mismatches. The efficiency of aligners can be improved using various heuristics, but the sensitivity and accuracy of the alignments are sacrificed. In this article, we introduce Basic Alignment tool for Mismatches (BatMis)—an efficient method to align short reads to a reference allowing k mismatches. BatMis is a Burrows–Wheeler transformation based aligner that uses a seed and extend approach, and it is an exact method.
Results:
Benchmark tests show that BatMis performs better than competing aligners in solving the k-mismatch problem. Furthermore, it can compete favorably even when compared with the heuristic modes of the other aligners. BatMis is a useful alternative for applications where fast k-mismatch mappings, unique mappings or multiple mappings of SGS data are required.
Availability and implementation:
BatMis is written in C/C++ and is freely available from http://code.google.com/p/batmis/
Contact:
ksung@comp.nus.edu.sg
Supplementary Information:
Supplementary information is available from Bioinformatics online.
Related Tools
FAIR Evaluation
Sorry, you must be signed in to evaluate this object.
