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/
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/
Authors: Hsiang-Chen Chou; Kuhulika Bhalla; Osama El Demerdesh; Olaf Klingbeil; Kaarina Hanington; Sergey Aganezov; Peter Andrews; Habeeb Alsudani; Kenneth Chang; Christopher R Vakoc; Michael C Schatz; W Richard McCombie; Bruce Stillman Journal: Elife Date: 2021-02-01 Impact factor: 8.140
Authors: Andrew R Bassett; Ghows Azzam; Lucy Wheatley; Charlotte Tibbit; Timothy Rajakumar; Simon McGowan; Nathan Stanger; Philip Andrew Ewels; Stephen Taylor; Chris P Ponting; Ji-Long Liu; Tatjana Sauka-Spengler; Tudor A Fulga Journal: Nat Commun Date: 2014-08-19 Impact factor: 14.919