Comparison of Sequencing Utility Programs

Comparison of Sequencing Utility Programs

Erik Aronesty, * Open Modal
Authors Info & Affiliations
The Open Bioinformatics Journal 31 Jan 2013 RESEARCH ARTICLE DOI: 10.2174/1875036201307010001


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.