title: AdapterRemoval v2: rapid adapter trimming, identification, and read merging.
abstract: BACKGROUND
  As high-throughput sequencing platforms produce longer and longer reads, sequences generated from short inserts, such as those obtained from fossil and degraded material, are increasingly expected to contain adapter sequences. Efficient adapter trimming algorithms are also needed to process the growing amount of data generated per sequencing run.
  
  
  RESULTS
  We introduce AdapterRemoval v2, a major revision of AdapterRemoval v1, which introduces (i) striking improvements in throughput, through the use of single instruction, multiple data (SIMD; SSE1 and SSE2) instructions and multi-threading support, (ii) the ability to handle datasets containing reads or read-pairs with different adapters or adapter pairs, (iii) simultaneous demultiplexing and adapter trimming, (iv) the ability to reconstruct adapter sequences from paired-end reads for poorly documented data sets, and (v) native gzip and bzip2 support.
  
  
  CONCLUSIONS
  We show that AdapterRemoval v2 compares favorably with existing tools, while offering superior throughput to most alternatives examined here, both for single and multi-threaded operations.
authors: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350, Copenhagen, Denmark. MikkelSch@gmail.com.
authors: Mikkel
authors: M
authors: Schubert
authors: Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen, Denmark. stinus.lindgreen@gmail.com.|Carlsberg Research Laboratory, Gamle Carlsberg Vej 4-10, 1799, Copenhagen, Denmark. stinus.lindgreen@gmail.com.
authors: Stinus
authors: S
authors: Lindgreen
authors: Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350, Copenhagen, Denmark. Lorlando@snm.ku.dk.|Laboratoire AMIS, Université de Toulouse, University Paul Sabatier (UPS), CNRS UMR 5288, 37 Allées Jules Guesde, 31000, Toulouse, France. Lorlando@snm.ku.dk.
authors: Ludovic
authors: L
authors: Orlando
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*