MEEPTOOLS: a maximum expected error based FASTQ read filtering and trimming toolkit
by Vishal N. Koparde; Hardik I. Parikh; Steven P. Bradley; Nihar U. Sheth
International Journal of Computational Biology and Drug Design (IJCBDD), Vol. 10, No. 3, 2017

Abstract: Quality-based sequence trimming of next generation sequencing (NGS) data is essential as it can potentially prevent missed or incorrect alignment downstream or prevent missassembly in a de novo assembly process by over-representing false k-mers. Trimming algorithms in tools like sickle, trimmomatic, etc. either depend on a running sum of quality of bases; or rely on average base quality of a sliding window. They consider PHRED quality, which is exponentially related to the probability of an erroneous base call. Here we present MEEPTOOLS, which is an open-source tool based on maximum expected error (MEE) as a percentage of read length (MEEP score) to filter, trim, truncate and assess NGS data in FASTQ file. By treating read trimming as a minimum subarray problem, MEEPTOOLS can simultaneously retain more reliable bases and remove unreliable bases than the traditional quality filtering strategies. MEEPTOOLS is ready available for download under the GNU GPLv3 at https://github.com/nisheth/meeptools.

Online publication date: Tue, 25-Jul-2017

The full text of this article is only available to individual subscribers or to users at subscribing institutions.

 
Existing subscribers:
Go to Inderscience Online Journals to access the Full Text of this article.

Pay per view:
If you are not a subscriber and you just want to read the full contents of this article, buy online access here.

Complimentary Subscribers, Editors or Members of the Editorial Board of the International Journal of Computational Biology and Drug Design (IJCBDD):
Login with your Inderscience username and password:

Username:        Password:          Forgotten your password?

Want to subscribe?
A subscription gives you complete access to all articles in the current issue, as well as to all articles in the previous three years (where applicable). See our Orders page to subscribe.

If you still need assistance, please email subs@inderscience.com