PhyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes.

ABSTRACT: The small-subunit rRNA (SSU rRNA) gene is the key marker in molecular ecology for all domains of life, but it is largely absent from metagenome-assembled genomes that often are the only resource available for environmental microbes. Here, we present phyloFlash, a pipeline to overcome this gap with rapid, SSU rRNA-centered taxonomic classification, targeted assembly, and graph-based binning of full metagenomic assemblies. We show that a cleanup of artifacts is pivotal even with a curated reference database. With such a filtered database, the general-purpose mapper BBmap extracts SSU rRNA reads five times faster than the rRNA-specialized tool SortMeRNA with similar sensitivity and higher selectivity on simulated metagenomes. Reference-based targeted assemblers yielded either highly fragmente

SUBMITTER: Gruber-Vodicka HR 

PROVIDER: S-EPMC7593591 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature