TY - JOUR AU - Treiber, Michelle L. AU - Taft, Diana H. AU - Korf, Ian AU - Mills, David A. AU - Lemay, Danielle G. PY - 2020 DA - 2020/02/24 TI - Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes JO - BMC Bioinformatics SP - 74 VL - 21 IS - 1 AB - 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. SN - 1471-2105 UR - https://doi.org/10.1186/s12859-020-3416-y DO - 10.1186/s12859-020-3416-y ID - Treiber2020 ER -