Comparison of Sequencing Utility Programs
Identifiers and Pagination:Year: 2013
First Page: 1
Last Page: 8
Publisher ID: TOBIOIJ-7-1
Article History:Received Date: 01/11/2012
Revision Received Date: 15/11/2012
Acceptance Date: 17/11/2012
Electronic publication date: 31/01/2013
Collection year: 2013
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.
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.