title: NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries.
abstract: CONCLUSIONS
  Illumina's recently released Nextera Long Mate Pair (LMP) kit enables production of jumping libraries of up to 12 kb. The LMP libraries are an invaluable resource for carrying out complex assemblies and other downstream bioinformatics analyses such as the characterization of structural variants. However, LMP libraries are intrinsically noisy and to maximize their value, post-sequencing data analysis is required. Standardizing laboratory protocols and the selection of sequenced reads for downstream analysis are non-trivial tasks. NextClip is a tool for analyzing reads from LMP libraries, generating a comprehensive quality report and extracting good quality trimmed and deduplicated reads.
  
  
  METHODS
  Source code, user guide and example data are available from https://github.com/richardmleggett/nextclip/.
authors.affiliation: The Genome Analysis Centre (TGAC), Norwich Research Park, Norwich NR4 7UH, UK.
authors.forename: Richard M
authors.initials: RM
authors.lastname: Leggett
authors.forename: Bernardo J
authors.initials: BJ
authors.lastname: Clavijo
authors.forename: Leah
authors.initials: L
authors.lastname: Clissold
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Clark
authors.forename: Mario
authors.initials: M
authors.lastname: Caccamo
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D029681:Arabidopsis Proteins / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D015698:Genomic Library; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D029681:Arabidopsis Proteins