AlienTrimmer removes adapter oligonucleotides with high sensitivity in short-insert paired-end reads. Commentary on Turner (2014) Assessment of insert sizes and adapter content in FASTQ data from NexteraXT libraries.

Alexis Criscuolo,Sylvain Brisse

doi:10.3389/fgene.2014.00130

Abstract

AlienTrimmer removes adapter oligonucleotides with high sensitivity in short-insert paired-end reads. Commentary on Turner (2014) Assessment of insert sizes and adapter content in FASTQ data from NexteraXT libraries.

Highlights

The bioinformatics protocol by Turner (2014) allows short-insert paired-end reads as well as library preparation oligonucleotides occurring within such reads to be identified
As underlined by Turner (2014), when the insert size is very short, each paired read is a composite sequence starting with genomic insert sequence in 5, whereas the downstream sequences contain oligonucleotides used for library preparation, followed by a short stretch of As, and by apparently random sequence with low Phred (Ewing and Green, 1998) quality scores Q
When the adapter oligonucleotide sequence is far from the 3 end because it is followed by unspecified index, primer or artefactual nucleotides, it is detected by AlienTrimmer but not trimmed off

Summary

Introduction

In a recent work, Turner (2014) compared the performances of two bioinformatics programs, cutadapt (Marcel, 2011) and AlienTrimmer (Criscuolo and Brisse, 2013), to trim off exogenous oligonucleotides from short-insert paired-end reads. Turner (2014) suggested that AlienTrimmer performed with very low sensitivity. In a recent work, Turner (2014) compared the performances of two bioinformatics programs, cutadapt (Marcel, 2011) and AlienTrimmer (Criscuolo and Brisse, 2013), to trim off exogenous oligonucleotides from short-insert paired-end reads. When all relevant oligonucleotide sequences to be trimmed off are specified, AlienTrimmer performs faster than cutadapt and with satisfactory sensitivity.

Results

Conclusion