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.
- 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