AnVIL: An overlap-aware genome assembly scaffolder for linked reads

10X Genomics Chromium linked reads contain information that can be used to link sequences together into scaffolds in draft genome assemblies. Existing software for this purpose perform the scaffolding by joining sequences together with a gap between them, not considering potential contig overlaps. Such overlaps can be particularly prominent in genome drafts assembled from long-read sequencing data where an overlap-layout-consensus (OLC) algorithm has been used. Ignoring overlapping contig ends may result in genes and other features being incomplete or fragmented in the resulting scaffolds.

We developed the application AnVIL to generate scaffolds from genome drafts using 10X Chromium data, with a focus on minimizing the number of gaps in resulting scaffolds by incorporating an OLC step to resolve junctions between linked contigs. We tested the performance of AnVIL on three published and simulated datasets and compared to the previously published tools ARCS and ARKS.

The results revealed that AnVIL performed similarly considering contiguity statistics, and the advantage of the overlapping step was revealed by fewer long and short variants in AnVIL produced scaffolds, in addition to a higher proportion of completely assembled LTR retrotransposons. We expect AnVIL to have broad applicability in genome assembly projects that utilize 10X Chromium linked reads.