EndHiC: assemble large contigs into chromosome-level scaffolds using the Hi-C links from contig ends

BMC Bioinformatics

Table 1 EndHiC consensus clusters for great burdock with robustness information

Cluster_id	Contig count	Cluster length (bp)	Robustness [max:90]	Included contigs with order and orientation
Cluster_A01	1	180,134,246	90	ptg000007l +
Cluster_A02	4	157,781,296	54	ptg000019l + ;ptg000017l + ;ptg000037l + ;ptg000033l-
Cluster_A03	2	137,502,900	81	ptg000003l + ;ptg000004l-
Cluster_A04	2	116,070,885	80	ptg000002l + ;ptg000026l +
Cluster_A05	1	103,325,058	90	ptg000009l +
Cluster_A06	1	98,139,150	90	ptg000005l +
Cluster_A07	2	91,022,879	90	ptg000020l + ;ptg000021l-
Cluster_A08	2	90,391,671	90	ptg000011l-;ptg000023l +
Cluster_A09	2	89,788,315	76	ptg000018l-;ptg000028l +
Cluster_A10	2	83,430,363	89	ptg000010l-;ptg000025l +
Cluster_A11	1	76,614,701	90	ptg000013l +
Cluster_A12	1	76,000,989	90	ptg000012l +
Cluster_A13	1	73,598,797	90	ptg000022l +
Cluster_A14	1	70,868,591	90	ptg000016l +
Cluster_A15	1	69,740,074	90	ptg000001l +
Cluster_A16	2	67,669,029	90	ptg000015l + ;ptg000027l-
Cluster_A17	1	61,985,296	90	ptg000008l +
Cluster_A18	1	60,844,256	90	ptg000014l +

This is the final merged cluster results from one round of EndHiC, with each cluster corresponding to a natural chromosome. Robustness represents the frequency of this cluster type in the EndHiC results of all parameter combinations. For the order and orientation of contigs, “+” stands for the forward strand, while “−” stands for the reverse strand

ISSN: 1471-2105