title: PEAT: an intelligent and efficient paired-end sequencing adapter trimming algorithm.
abstract: BACKGROUND
  In modern paired-end sequencing protocols short DNA fragments lead to adapter-appended reads. Current paired-end adapter removal approaches trim adapter by scanning the fragment of adapter on the 3' end of the reads, which are not competent in some applications.
  
  
  RESULTS
  Here, we propose a fast and highly accurate adapter-trimming algorithm, PEAT, designed specifically for paired-end sequencing. PEAT requires no a priori adaptor sequence, which is convenient for large-scale meta-analyses. We assessed the performance of PEAT with many adapter trimmers in both simulated and real life paired-end sequencing libraries. The importance of adapter trimming was exemplified by the influence of the downstream analyses on RNA-seq, ChIP-seq and MNase-seq. Several useful guidelines of applying adapter trimmers with aligners were suggested.
  
  
  CONCLUSIONS
  PEAT can be easily included in the routine paired-end sequencing pipeline. The executable binaries and the standalone C++ source code package of PEAT are freely available online.
authors.forename: Yun-Lung
authors.initials: YL
authors.lastname: Li
authors.forename: Jui-Cheng
authors.initials: JC
authors.lastname: Weng
authors.forename: Chiung-Chih
authors.initials: CC
authors.lastname: Hsiao
authors.forename: Min-Te
authors.initials: MT
authors.lastname: Chou
authors.forename: Chin-Wen
authors.initials: CW
authors.lastname: Tseng
authors.forename: Jui-Hung
authors.initials: JH
authors.lastname: Hung
mesh_terms: D000465:Algorithms; D047369:Chromatin Immunoprecipitation; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA; D012984:Software; D013997:Time Factors