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NxTrim: optimized trimming of Illumina mate pair reads

By Jared O’Connell, Ole Schulz-Trieglaff, Emma Carlson, Matthew M Hims, Niall A Gormley, Anthony J. Cox

Posted 06 Aug 2014
bioRxiv DOI: 10.1101/007666 (published DOI: 10.1093/bioinformatics/btv057)

Motivation: Mate pair protocols add to the utility of paired-end sequencing by boosting the genomic distance spanned by each pair of reads, potentially allowing larger repeats to be bridged and resolved. The Illumina Nextera Mate Pair (NMP) protocol employs a circularisation-based strategy that leaves behind 38bp adapter sequences which must be computationally removed from the data. While "adapter trimming" is a well-studied area of bioinformatics, existing tools do not fully exploit the particular properties of NMP data and discard more data than is necessary. Results: We present NxTrim, a tool that strives to discard as little sequence as possible from NMP reads. The sequence either side of the adapter site is triaged into "virtual libraries" of mate pairs, paired-end reads and single-ended reads. When combined, these data boost coverage and can substantially improve the de novo assembly of bacterial genomes.

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