ALIENTRIMMER: a tool to quickly and accurately trim off multipleshort contaminant sequences from high-throughput sequencing reads

Criscuolo A, Brisse S (2013) ALIENTRIMMER: a tool to quickly and accurately trim off multipleshort contaminant sequences from high-throughput sequencing reads. Genomics. 102:500-506.doi:10.1016/j.ygeno.2013.07.011ftp://ftp.pasteur.fr/pub/GenSoft/projects/AlienTrimmer/

AlienTrimmer is a program that allows detecting and removing sequencing errors andcontaminant sequences (e.g. adaptors, primers) in both ends of high-throughput sequencing(HTS) read sequences. Based on the decomposition of the specified alien sequences intonucleotide k-mers of fixed length k, AlienTrimmer is able to determine whether such alienk-mers are occurring in both read ends by using a simple polynomial algorithm.AlienTrimmer can process typical HTS single- or paired-ends read files containingmillions entries in few minutes with very low computer resources.

CHANGESINVERSION 0.4.0•by default, quality-based trimming is performed along with alien trimming (Phred qualityscore cut-off = 20)•Phred quality score cut-off is specified with numerical value (Phred score encoding isautomatically assessed from input FASTQ files

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