Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes.

ABSTRACT:

Background

Shotgun metagenomes are often assembled prior to annotation of genes which biases the functional capacity of a community towards its most abundant members. For an unbiased assessment of community function, short reads need to be mapped directly to a gene or protein database. The ability to detect genes in short read sequences is dependent on pre- and post-sequencing decisions. The objective of the current study was to determine how library size selection, read length and format, protein database, e-value threshold, and sequencing depth impact gene-centric analysis of human fecal microbiomes when using DIAMOND, an alignment tool that is up to 20,000 times faster than BLASTX.

Results

Using metagenomes simulated from a database of experimentally verified protein sequ

SUBMITTER: Treiber ML 

PROVIDER: S-EPMC7041091 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature