PT  - JOURNAL ARTICLE
AU  - Jared O’Connell
AU  - Ole Schulz-Trieglaff
AU  - Emma Carlson
AU  - Matthew M. Hims
AU  - Niall A. Gormley
AU  - Anthony J. Cox
TI  - NxTrim: optimized trimming of Illumina mate pair reads
AID  - 10.1101/007666
DP  - 2014 Jan 01
TA  - bioRxiv
PG  - 007666
4099  - http://biorxiv.org/content/early/2014/08/06/007666.short
4100  - http://biorxiv.org/content/early/2014/08/06/007666.full
AB  - 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.Availability The source code is available at https://github.com/sequencing/NxTrimContact acox{at}illumina.com