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

Frontiers in Genetics

Volumn 5, Issue MAY, 2014, Pages

  Criscuolo, Alexis ^a,b,c   Brisse, Sylvain ^a,c  

^a INSTITUT PASTEUR   (France)

^b CEMAGREF   (France)

^c CNRS   (France)

Author keywords

Alien trimmer; Cutadapt; Index; Insert; Paired end reads; Primer; transposase sequence

Indexed keywords

EID: 84905671835     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2014.00130     Document Type: Note

References (5)

1. Bolger, A. M., Lohsel, M., and Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. doi: 10.1093/bioinformatics/btu170. [Epub ahead of print].
2. Criscuolo, A., and Brisse, S. (2013). AlienTrimmer: a tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads. Genomics 102, 500-506. doi: 10.1016/j.ygeno.2013.07.011
3. Ewing, B., and Green, P. (1998). Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8, 186-194.
4. Marcel, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17, 10-12. doi: 10.14806/ej.17.1.200
5. Turner, F. S. (2014). Assessment of insert sizes and adapter content in FASTQ data from NexteraXT libraries. Front. Genet. 5:5. doi: 10.3389/fgene.2014.00005