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bioRxiv · 10.1101/284596

BisPin and BFAST-Gap: Mapping Bisulfite-Treated Reads

Porter, J.·Zhang, L.
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Abstract

BackgroundBisPin is a new multiprocess bisulfite-treated short DNA read mapper written in Python 2.7. It performs alignments using BFAST, leveraging its multithreading functionality and thorough hash-based indexing strategy. BisPin is feature rich and supports directional, nondirectional, PBAT, and hairpin construction strategies. BisPin approaches read mapping by converting the Cs to Ts and the Gs to As in both the reads and the reference genome. BisPin uses fast rescoring to disambiguate ambiguously aligned reads for a superior amount of uniquely mapped reads compared to other mappers. The performance of BisPin was evaluated on both real and simulated data in comparison to other read mappers.\n\nBFAST-Gap is a modified version of BFAST meant for Ion Torrent reads. It uses a parameterized logistic function to determine the weights of the gap open and extension penalties based on the homopolymer run length of the DNA read. This is because the Ion Torrent sequencing technology can overcall and undercall homopolymer runs. BisPin works with both BFAST-Gap and BFAST. BFAST-Gap is compatible with indexes built with BFAST. There are few mappers that specifically address Ion Torrent data. BFAST-Gap works with Illumina reads as well.\n\nResultsBisPin with BFAST consistently had a higher amount of uniquely mapped reads compared to other mappers on real data using a variety of construction strategies. Using a hairpin validation strategy, BisPin was superior using the maximum score, and it mapped 73% of reads correctly.\n\nBisPin with BFAST-Gap on Ion Torrent reads with a logistic gap open penalty function improved mapping accuracy with real and simulated data. On simulated bisulfite Ion Torrent data, the area under the curve was improved by approximately seven, and on one real data set, the uniquely mapped percent was improved by seven percent. BFAST-Gap performed better than TMAP on simulated regular Ion Torrent reads, and TMAP is designed for Ion Torrent reads. Other read mappers had worse performance.\n\nConclusionsBisPin and BFAST-Gap have consistently good accuracy with a variety of data. BisPin is feature-rich. This makes BisPin and BFAST-Gap useful additions to read mapping software.

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Porter, J., Zhang, L.. 2018-03-19. BisPin and BFAST-Gap: Mapping Bisulfite-Treated Reads. https://doi.org/10.1101/284596

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