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Concatenation of Paired-end Reads Improves Taxonomic Classification of Amplicons for Profiling Microbial Communities by Daniel P. Dacey; Frédéric J. J. Chain is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.

What is Concatenation of Paired-end Reads Improves Taxonomic Classification of Amplicons for Profiling Microbial Communities about?

## Abstract ## Background Taxonomic classification of genetic markers for microbiome analysis is affected by the numerous choices made from sample preparation to bioinformatics analysis. Paired-end read merging is routinely used to capture the entire amplicon sequence when the read ends overlap. However, the exclusion of unmerged reads from further analysis can result in underestimating the diversity in the sequenced microbial community and is influenced by bioinformatic processes such as read trimming and the choice of reference database. A potential solution to overcome this is to concatenate (join) reads that do not overlap and keep them for taxonomic classification. The use of concatenated reads can outperform taxonomic recovery from single-end reads, but it remains unclear how their performance compares to merged reads. Using various sequenced mock communities with different amplicons, read length, read depth, taxonomic composition, and sequence quality, we tested how merging and concatenating reads performed for genus recall and precision in bioinformatic pipelines combining different parameters for read trimming and taxonomic classification using different reference database

Who reads Concatenation of Paired-end Reads Improves Taxonomic Classification of Amplicons for Profiling Microbial Communities?

Author

Daniel P. Dacey; Frédéric J. J. Chain

Publisher

Springer Science and Business Media LLC

Published

2021

Language

EN

Field

Biochemistry, Genetics and Molecular Biology (Life Sciences)