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NextClip is a tool for comprehensive quality analysis and read preparation for Nextera long mate pair (LMP) libraries. NextClip comprises two parts. The core component is the NextClip command line tool, an efficient C program for processing mate pair FASTQ files, generating summary statistics and preparing reads for use in scaffolding. A second component, the NextClip pipeline, is designed for cases where there is a reference of partially assembly. It utilises NextClip, along with BWA, to generate a more detailed PDF report that includes analysis of library insert sizes.

NextClip will:

  • Look for the presence of the junction adaptor and categorise reads according to its presence in one, both or neither read.
  • Look for external adaptors.
  • Clip reads before adaptors.
  • Assess the orientation (MP, PE, tandem) of each read.
  • Produce insert size histograms.
  • Assess GC content graphs and ambiguous bases.
  • Produce histograms of clipped read length.
  • Examine PCR duplication rates and remove duplicates if required.

NextClip is open source. Software and documentation are available from the links below. Published as:

NextClip: an analysis and read preparation tool for Nextera long mate pair libraries
Richard M. Leggett; Bernardo J. Clavijo; Leah Clissold; Matthew D. Clark; Mario Caccamo
Bioinformatics 2013; doi: 10.1093/bioinformatics/btt702




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