MeFiT: Merging and Filtering Tool for Illumina Paired-end Reads for 16S RRNA Amplicon Sequencing

Overview

Journal BMC Bioinformatics

Publisher Biomed Central

Specialty Biology

Date 2016 Dec 2

PMID 27905885

Citations 47

Authors

Hardik I Parikh

Vishal N Koparde

Steven P Bradley

Gregory A Buck

Nihar U Sheth

Affiliations

Soon will be listed here.

Abstract

Background: Recent advances in next-generation sequencing have revolutionized genomic research. 16S rRNA amplicon sequencing using paired-end sequencing on the MiSeq platform from Illumina, Inc., is being used to characterize the composition and dynamics of extremely complex/diverse microbial communities. For this analysis on the Illumina platform, merging and quality filtering of paired-end reads are essential first steps in data analysis to ensure the accuracy and reliability of downstream analysis.

Results: We have developed the Merging and Filtering Tool (MeFiT) to combine these pre-processing steps into one simple, intuitive pipeline. MeFiT invokes CASPER (context-aware scheme for paired-end reads) for merging paired-end reads and provides users the option to quality filter the reads using the traditional average Q-score metric or using a maximum expected error cut-off threshold.

Conclusions: MeFiT provides an open-source solution that permits users to merge and filter paired end illumina reads. The tool has been implemented in python and the source-code is freely available at https://github.com/nisheth/MeFiT .

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