Genetic data was first sequenced using the standard Illumina protocol. After sequencing, kmer analysis was performed to estimate genome size (1.32 Gb), level of heterozygosity (-52x), and repeat content of the sequenced genome. JellyFish was used to extract 17-mers from the WGS PE reads, unique kmers were identified and counted according to kmer depth. To address the challenge of distinguishing divergent alleles of the same locus from true repeats, 96 sequenced fosmid pools were assembled to obtain 96 largely haploid assemblies. For each pool a base assembly was produced using ABySSv1.3.7 and parameters: −s 300 − S 300–5000 − n 9 − N 15 − k 97 − l 75 − aligner map − q 10. Afterwords, the base assemblies went through several rounds of gapfilling, decontamination, consistency checks, and rescaffolding with ABySSv1.3.7. The 96 fosmid pool assemblies then went through two rounds of merging based on overlaps using in-house OLC-like assembly-merging software called ASM.
Source:
https://gigascience.biomedcentral.com/articles/10.1186/s13742-016-0134-5#Bib1
