Lyrebird

Lyrebird is a module of SingleM specialized towards the profiling of viruses in metagenomic data. Currently, Lyrebird profiles dsDNA phages belonging to the Caudoviricetes. Lyrebird is similar to standard microbial SingleM, with some main conceptual differences: Since phage lack universal single copy marker genes, Lyrebird uses an expanded set of >500 marker genes, and does not assume each of them is present in each phage. Lyrebird uses a more sensitive homology search method to recruit reads to marker gene windows. Lyrebird does not use GTDB taxonomy, but instead uses a custom taxonomy based on vConTACT3 analysis of a custom collection of reference sequences derived from ICTV and IMG-VR.