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. 2016 Dec 1;17(1):491.
doi: 10.1186/s12859-016-1358-1.

MeFiT: merging and filtering tool for illumina paired-end reads for 16S rRNA amplicon sequencing

Hardik I Parikh  1 , Vishal N Koparde  2 , Steven P Bradley  1 , Gregory A Buck  1   2 , Nihar U Sheth  3
Affiliations

MeFiT: merging and filtering tool for illumina paired-end reads for 16S rRNA amplicon sequencing

Hardik I Parikh et al. BMC Bioinformatics. .

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 .

Keywords: 16S rRNA; microbiome; paired-end sequencing; pre-processing; quality filtering.

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Figures

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Fig. 1
The MeFiT pipeline
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