Introduction

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 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.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 .

Publications

  1. MeFiT: merging and filtering tool for illumina paired-end reads for 16S rRNA amplicon sequencing.
    Cite this
    Parikh HI, Koparde VN, Bradley SP, Buck GA, Sheth NU, 2016-12-01 - BMC bioinformatics

Credits

  1. Hardik I Parikh
    Developer

    Department of Microbiology and Immunology, Virginia Commonwealth University, United States of America

  2. Vishal N Koparde
    Developer

    Center for the Study of Biological Complexity, Virginia Commonwealth University, United States of America

  3. Steven P Bradley
    Developer

    Department of Microbiology and Immunology, Virginia Commonwealth University, United States of America

  4. Gregory A Buck
    Developer

    Center for the Study of Biological Complexity, Virginia Commonwealth University, United States of America

  5. Nihar U Sheth
    Investigator

    Center for the Study of Biological Complexity, Virginia Commonwealth University, United States of America

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Summary
AccessionBT006490
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByNihar U Sheth