title: MeFiT: merging and filtering tool for illumina paired-end reads for 16S rRNA amplicon sequencing.
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 .
authors.affiliation: Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, USA.
authors.forename: Hardik I
authors.initials: HI
authors.lastname: Parikh
authors.affiliation: Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, USA.
authors.forename: Vishal N
authors.initials: VN
authors.lastname: Koparde
authors.affiliation: Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, USA.
authors.forename: Steven P
authors.initials: SP
authors.lastname: Bradley
authors.affiliation: Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, USA.|Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, USA.
authors.forename: Gregory A
authors.initials: GA
authors.lastname: Buck
authors.affiliation: Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, USA. nsheth@vcu.edu.
authors.forename: Nihar U
authors.initials: NU
authors.lastname: Sheth
mesh_terms: D001419:Bacteria / Q000235:genetics; D005798:Genes, Bacterial; D020459:Genes, rRNA; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D012336:RNA, Ribosomal, 16S
keywords: 16S rRNA; microbiome; paired-end sequencing; pre-processing; quality filtering