phyloFlash -- Rapid SSU rRNA profiling and targeted assembly from metagenomes

Abstract

The SSU rRNA gene is the key marker in molecular ecology for all domains of life, but 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 fragmented assemblies or high levels of chimerism, so we employ the general-purpose genomic assembler SPAdes. Our optimized implementation is independent of reference database composition and has satisfactory levels of chimera formation. Using the phyloFlash workflow we could recover the first complete genomes of several enigmatic taxa, including Marinamargulisbacteria from surface ocean seawater. phyloFlash quickly processes Illumina (meta)genomic data, is straightforward to use, even as part of high-throughput quality control, and has user-friendly output reports. The software is available at https://github.com/HRGV/phyloFlash (GPL3 license) and is documented with an online manual.