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Generating amplicon reads for microbial community assessment with next‐generation sequencing
Author(s) -
Gołębiewski M.,
Tretyn A.
Publication year - 2020
Publication title -
journal of applied microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.889
H-Index - 156
eISSN - 1365-2672
pISSN - 1364-5072
DOI - 10.1111/jam.14380
Subject(s) - amplicon sequencing , amplicon , pipeline (software) , dna sequencing , computational biology , whole genome sequencing , biology , computer science , genome , genetics , gene , polymerase chain reaction , 16s ribosomal rna , programming language
Summary Marker gene amplicon sequencing is often preferred over whole genome sequencing for microbial community characterization, due to its lower cost while still enabling assessment of uncultivable organisms. This technique involves many experimental steps, each of which can be a source of errors and bias. We present an up‐to‐date overview of the whole experimental pipeline, from sampling to sequencing reads, and give information allowing for informed choices at each step of both planning and execution of a microbial community assessment study. When applicable, we also suggest ways of avoiding inherent pitfalls in amplicon sequencing.