NextClip

NextClip

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.

Paper

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 (2014). Bioinformatics 30(4):566-568.

GitHub

NextClip

Documentation

https://documentation.tgac.ac.uk/

Issue tracker

https://tracker.tgac.ac.uk/