Table 1.

Comparison of the assemblies of the AC by different strategies

	Direct assembly of AC from WGS reads	Assembly of AC after filtering out reads of worm genomic sequence	Assembly of AC after filtering out reads of worm genomic sequence + polish after assembly
Contig number	66	50	49
Total length	10 922 164 bp	10 813 732 bp	11 072 328 bp
N50	418 241 bp	691 347 bp	710 368 bp
Longest contig	1 487 696 bp	1 706 458 bp	1 746 823 bp

AC contigs were assembled directly along with endogenous chromosomes, assembled alone after excluding worm genomic sequences, as outlined in Supplementary Figure S4B, or assembled alone plus polishing after assembly by nanopore and Mi-seq reads.