RESEARCH ARTICLE


Comparison of Sequencing Utility Programs



Erik Aronesty*
Expression Analysis, A Quintiles Company, Durham, NC, USA


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Creative Commons License
© 2013 Erik Aronesty

open-access license: This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International Public License (CC-BY 4.0), a copy of which is available at: https://creativecommons.org/licenses/by/4.0/legalcode. This license permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

* Address correspondence to this author at the Expression Analysis, a Quintiles Company, Durham, NC, USA; Tel: 919-287-4011; E-mail: erik.aronesty@quintiles.com


Abstract

High throughput sequencing (HTS) has resulted in extreme growth rates of sequencing data. At our lab, we generate terabytes of data every day. It is usually seen as required for data output to be “cleaned” and processed in various ways prior to use for common tasks such as variant calling, expression quantification and assembly.

Two common tasks associated with HTS are adapter trimming and paired-end joining. I have developed two tools at Expression Analysis, Inc. to address these common tasks. The names of these programs are fastq-mcf and fastq-join. I compared the performance of these tools to similar open-source utilities, both in terms of resource efficiency, and effectiveness.

Keywords: Sequencing, utilities, Illumina, clipping, ngs and next-generation.