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

BMC Bioinformatics

Software

Vishal N. Koparde¹  Nihar U. Sheth¹  Steven P. Bradley²  Hardik I. Parikh²  Gregory A. Buck³ 

[1] Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, USA;Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, USA;Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, USA;Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, USA;

关键词: 16S rRNA;    microbiome;    paired-end sequencing;    quality filtering;    pre-processing;   

DOI  :  10.1186/s12859-016-1358-1

 received in 2016-06-11, accepted in 2016-11-19,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundRecent 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.ResultsWe 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.ConclusionsMeFiT 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.

【 授权许可】

CC BY   
© The Author(s). 2016