MeFiT: merging and filtering tool for illumina paired-end reads for 16S rRNA amplicon sequencing.
BMC Bioinformatics
; 17(1): 491, 2016 Dec 01.
Article
em En
| MEDLINE
| ID: mdl-27905885
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 .Palavras-chave
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Software
/
RNA Ribossômico 16S
/
Análise de Sequência de DNA
/
Genes de RNAr
/
Genômica
/
Genes Bacterianos
Idioma:
En
Ano de publicação:
2016
Tipo de documento:
Article