title: NxTrim: optimized trimming of Illumina mate pair reads.
abstract: BACKGROUND
  Mate pair protocols add to the utility of paired-end sequencing by boosting the genomic distance spanned by each pair of reads, potentially allowing larger repeats to be bridged and resolved. The Illumina Nextera Mate Pair (NMP) protocol uses a circularization-based strategy that leaves behind 38-bp adapter sequences, which must be computationally removed from the data. While 'adapter trimming' is a well-studied area of bioinformatics, existing tools do not fully exploit the particular properties of NMP data and discard more data than is necessary.
  
  
  RESULTS
  We present NxTrim, a tool that strives to discard as little sequence as possible from NMP reads. NxTrim makes full use of the sequence on both sides of the adapter site to build 'virtual libraries' of mate pairs, paired-end reads and single-ended reads. For bacterial data, we show that aggregating these datasets allows a single NMP library to yield an assembly whose quality compares favourably to that obtained from regular paired-end reads.
  
  
  METHODS
  The source code is available at https://github.com/sequencing/NxTrim
authors: Computational Biology Group and Technology Development, Illumina Cambridge Ltd., Chesterford Research Park, Little Chesterford, Essex CB10 1XL, UK.
authors: Jared
authors: J
authors: O'Connell
authors: Computational Biology Group and Technology Development, Illumina Cambridge Ltd., Chesterford Research Park, Little Chesterford, Essex CB10 1XL, UK.
authors: Ole
authors: O
authors: Schulz-Trieglaff
authors: Computational Biology Group and Technology Development, Illumina Cambridge Ltd., Chesterford Research Park, Little Chesterford, Essex CB10 1XL, UK.
authors: Emma
authors: E
authors: Carlson
authors: Computational Biology Group and Technology Development, Illumina Cambridge Ltd., Chesterford Research Park, Little Chesterford, Essex CB10 1XL, UK.
authors: Matthew M
authors: MM
authors: Hims
authors: Computational Biology Group and Technology Development, Illumina Cambridge Ltd., Chesterford Research Park, Little Chesterford, Essex CB10 1XL, UK.
authors: Niall A
authors: NA
authors: Gormley
authors: Computational Biology Group and Technology Development, Illumina Cambridge Ltd., Chesterford Research Park, Little Chesterford, Essex CB10 1XL, UK.
authors: Anthony J
authors: AJ
authors: Cox
mesh_terms: D001419:Bacteria / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D015723:Gene Library; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software