MeFiT: Merging and Filtering Tool for Illumina Paired-End Reads for 16S rRNA Amplicon Sequencing

TL;DR

MeFiT is an open-source Python tool that simplifies merging and filtering Illumina paired-end reads for 16S rRNA sequencing, improving data quality for microbial community analysis.

Contribution

It introduces a unified, user-friendly pipeline for merging and filtering Illumina paired-end reads, enhancing preprocessing efficiency in microbial genomics.

Findings

Provides an open-source, easy-to-use tool for read merging and filtering.

Supports customizable quality parameters for improved data accuracy.

Facilitates more reliable downstream microbial community analysis.

Abstract

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. We have developed the Merging and Filtering Tool (MeFiT) to combine these pre-processing steps into one simple, intuitive pipeline. MeFiT provides an open-source solution that permits users to merge and filter paired end illumina reads based on user-selected quality parameters. The tool has been implemented in python and the source-code is freely available at https://github.com/nisheth/MeFiT.