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BatAlign: an incremental method for accurate alignment of sequencing reads
- Source :
- Nucleic Acids Research
- Publication Year :
- 2015
-
Abstract
- Structural variations (SVs) play a crucial role in genetic diversity. However, the alignments of reads near/across SVs are made inaccurate by the presence of polymorphisms. BatAlign is an algorithm that integrated two strategies called ‘Reverse-Alignment’ and ‘Deep-Scan’ to improve the accuracy of read-alignment. In our experiments, BatAlign was able to obtain the highest F-measures in read-alignments on mismatch-aberrant, indel-aberrant, concordantly/discordantly paired and SV-spanning data sets. On real data, the alignments of BatAlign were able to recover 4.3% more PCR-validated SVs with 73.3% less callings. These suggest BatAlign to be effective in detecting SVs and other polymorphic-variants accurately using high-throughput data. BatAlign is publicly available at https://goo.gl/a6phxB.
Details
- ISSN :
- 13624962
- Volume :
- 43
- Issue :
- 16
- Database :
- OpenAIRE
- Journal :
- Nucleic acids research
- Accession number :
- edsair.doi.dedup.....3776029854469ec4c3074f2eac5bf053