Table 1.

Preprocessing alignment tools.

Name	Site	Description	Authors
Fastx-toolkit	http://hannonlab.cshl.edu/fastx_toolkit/	FASTA/FASTQ file processing	Gordon and Hannon (unpublished)
QC tools	http://www.nipgr.res.in/ngsqctoolkit.html	Ilumina and Roche 454 FASTQ file processing	Patel and Jain (2012)
Cutadapt	http://code.google.com/p/cutadapt/	Removes adapter sequence	Martin (2011)
ShortRead	http://bioconductor.org/packages/2.10/bioc/html/ShortRead.html	FASTA/FASTQ file processing	Morgan et al. (2009)
Biostrings	http://bioconductor.org/packages/2.10/bioc/html/Biostrings.html	String objects representing biological sequences, and matching algorithms	Pàges et al. (2012); R package version 2.24.1