Fig. 1

Types of assembled contigs and alignments to REF contigs. a A contig pair is a pair of contigs which are the only contigs originating from a single scaffold. b Some scaffolds contain “N”s that denote scaffolding of contigs from pairs of reads or linked reads with common barcodes. After removal of “N”s, the remaining sequences are termed LR contigs or REF contigs, depending on the origin of the scaffold. Removal of 40 bases from both ends of an LR contig results in a trimmed LR contig. c Trimmed or untrimmed LR contigs are aligned to the REF contigs. Alignments are categorized as fully aligned, where the entire contig aligns to a REF contig; alignments with tails, where a region of the LR contig aligns to a REF contig but a region at either or both ends of the LR contig does not align to the REF contig; or uncategorized, where the LR contig extends past the edge of a REF contig. d LR contigs with tails are divided into two regions: the aligned region and the tail region. Tails can be removed in silico to generate a set of tail-derived contigs. e LR contigs with tails that fully align to a unique location in the genome on the same or a different REF contig are termed chimeric LR contigs