ArticleBMC bioinformatics2016
MeFiT: merging and filtering tool for illumina paired-end reads for 16S rRNA amplicon sequencing.
Article in BMC bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed.
- Trial
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- Presepsin as a biomarker of bacterial translocation and an indicator for the prescription of probiotics in cirrhosis.World journal of hepatology · 2024Article
- Gut Microbiota and Biomarkers of Intestinal Barrier Damage in Cirrhosis.Microorganisms · 2024Article
- ITS and 16S rDNA metagenomic dataset of different soils from flax fields.Data in brief · 2024Article
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- Antibody Response to the Sneathia vaginalis Cytopathogenic Toxin A during Pregnancy.ImmunoHorizons · 2024Article
- Effect of Rebamipide on the Intestinal Barrier, Gut Microbiota Structure and Function, and Symptom Severity Associated with Irritable Bowel Syndrome and Functional Dyspepsia Overlap: A Randomized Controlled Trial.Journal of clinical medicine · 2023Article
- Gut Dysbiosis and Hemodynamic Changes as Links of the Pathogenesis of Complications of Cirrhosis.Microorganisms · 2023Article
- Article
- The Effect of the MicroalgaeMicroorganisms · 2023Article
- Eubiotic effect of rifaximin is associated with decreasing abdominal pain in symptomatic uncomplicated diverticular disease: results from an observational cohort study.BMC gastroenterology · 2023Observational
- Organic and inorganic nutrients modulate taxonomic diversity and trophic strategies of small eukaryotes in oligotrophic oceans.FEMS microbes · 2023Article
- Microbiome data reveal significant differences in the bacterial diversity in freshwater rohu (Labeo rohita) across the supply chain in Dhaka, Bangladesh.Letters in applied microbiology · 2022Article
- Race, the Vaginal Microbiome, and Spontaneous Preterm Birth.mSystems · 2022Article
- Gut dysbiosis and body composition in cirrhosis.World journal of hepatology · 2022Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
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 .
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.