Extended Data Fig. 2: VGP assembly pipeline applied across multiple species.

a, Iterative assembly pipeline of sequence data types (coloured as in b) with increasing chromosomal distance. Thin bars, sequence reads; thick black bars, assembled contigs; black bars with space and arcing links, scaffolds; grey bars, gaps placed by previous steps; thick red border, tracking of an example contig in the pipeline. The curation step shows an example of a mis-assembly break identified by sequence coverage (grey, left) and an example of an inversion error (right) detected by the optical map. b, Intra-molecule length distribution of the four data types used to generate the assemblies of 16 vertebrate species, weighted by the fraction of bases in each length bin (log scaled). Molecule length above 1 kb was measured from read length for CLR, estimated molecule coverage for linked reads, raw molecule length for optical maps, and interaction distance for Hi-C reads. For each species, the fragment length distribution of each data type was similar to those for the Anna’s hummingbird, with differences primarily influenced by tissue type, preservation method, and collection or storage conditions (unpublished data).