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

Hardik I. Parikh, Vishal N. Koparde, Steven P. Bradley, Gregory A. Buck, Nihar U. Sheth
2016 BMC Bioinformatics  
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.
more » ... ts: 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.
doi:10.1186/s12859-016-1358-1 pmid:27905885 pmcid:PMC5134250 fatcat:qrsocgl5jfg2zk65osmv4bujrm