2.3 Assignment of scaffolds to chromosomes
A. flavipes Hi-C libraries from liver tissue were prepared, as described previously (Lieberman-Aiden et al., 2009). Hi-C libraries were sequenced on the BGISEQ-500 platform and quality controlled using the HiC-Pro (v2.8.0_devel) (Servant et al., 2015) pipeline, resulting in 51.0 Gb uniquely aligned read pairs. Reads validated by HiC-Pro were next used to scaffold contigs into seven chromosome clusters (2n =14 karyotype) using the 3D-DNA v1.12 pipeline (O. Dudchenko et al., 2017). The assembly was further improved by interactive correction using Juicebox v1.11.08 (Olga Dudchenko et al., 2018; Durand et al., 2016). A chromatin contact map can be found in Figure S2 .