NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 24297520.
- Also identified by DOI 10.1093/bioinformatics/btt702 and PMC identifier 3928519.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
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. Source code, user guide and example data are available from https://github.com/richardmleggett/nextclip/.
Medical subject headings
- Arabidopsis Proteins
- Computational Biology
- Genomic Library
- High-Throughput Nucleotide Sequencing
- Sequence Analysis, DNA
- Software