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

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/.

SUBMITTER: Leggett RM

PROVIDER: S-EPMC3928519 | biostudies-literature | 2014 Feb

REPOSITORIES: biostudies-literature

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

Leggett Richard M RM Clavijo Bernardo J BJ Clissold Leah L Clark Matthew D MD Caccamo Mario M

Bioinformatics (Oxford, England) 20131202 4

<h4>Summary</h4>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 re ...[more]

PMID: 24297520

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