title: ResSeq: Enhancing Short-Read Sequencing Alignment By Rescuing Error-Containing Reads.
abstract: Next-generation short-read sequencing is widely utilized in genomic studies. Biological applications require an alignment step to map sequencing reads to the reference genome, before acquiring expected genomic information. This requirement makes alignment accuracy a key factor for effective biological interpretation. Normally, when accounting for measurement errors and single nucleotide polymorphisms, short read mappings with a few mismatches are generally considered acceptable. However, to further improve the efficiency of short-read sequencing alignment, we propose a method to retrieve additional reliably aligned reads (reads with more than a pre-defined number of mismatches), using a Bayesian-based approach. In this method, we first retrieve the sequence context around the mismatched nucleotides within the already aligned reads; these loci contain the genomic features where sequencing errors occur. Then, using the derived pattern, we evaluate the remaining (typically discarded) reads with more than the allowed number of mismatches, and calculate a score that represents the probability that a specific alignment is correct. This strategy allows the extraction of more reliably aligned reads, therefore improving alignment sensitivity.
  
  
  METHODS
  The source code of our tool, ResSeq, can be downloaded from: https://github.com/hrbeubiocenter/Resseq.
authors.forename: Weixing
authors.initials: W
authors.lastname: Feng
authors.forename: Peichao
authors.initials: P
authors.lastname: Sang
authors.forename: Deyuan
authors.initials: D
authors.lastname: Lian
authors.forename: Yansheng
authors.initials: Y
authors.lastname: Dong
authors.forename: Fengfei
authors.initials: F
authors.lastname: Song
authors.forename: Meng
authors.initials: M
authors.lastname: Li
authors.forename: Bo
authors.initials: B
authors.lastname: He
authors.forename: Fenglin
authors.initials: F
authors.lastname: Cao
authors.forename: Yunlong
authors.initials: Y
authors.lastname: Liu
mesh_terms: D001499:Bayes Theorem; D019295:Computational Biology / Q000379:methods*; D004269:DNA, Bacterial / Q000032:analysis / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial