Fig. 1

Assembly workflow and sampling bias estimates show GC% discrepancies in long-read vs short-read assemblies. Using the same sample from a cannulated cow, (a) we extracted DNA using a modified bead beating protocol that still preserved a large proportion of high molecular weight DNA strands. This DNA extraction was sequenced on a short-read sequencer (Illumina; dark green) and a long-read sequencer (PacBio RSII and Sequel; dark orange), with each sequence source assembled separately. Assessments of read- and contig-level GC% bias (b) revealed that a substantial proportion of sampled low GC DNA was not incorporated into either assembly. c Assembly contigs were annotated for likely superkingdoms of origin and were compared for overall contig lengths. The long-read assembly tended to have longer average contigs for each assembled superkingdom compared to the short-read assembly