Format

Send to

Choose Destination
Bioinformatics. 2014 Feb 15;30(4):566-8. doi: 10.1093/bioinformatics/btt702. Epub 2013 Dec 2.

NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries.

Author information

1
The Genome Analysis Centre (TGAC), Norwich Research Park, Norwich NR4 7UH, UK.

Abstract

SUMMARY:

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.

AVAILABILITY AND IMPLEMENTATION:

Source code, user guide and example data are available from https://github.com/richardmleggett/nextclip/.

PMID:
24297520
PMCID:
PMC3928519
DOI:
10.1093/bioinformatics/btt702
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center