Puzzle Hi-C: An accurate scaffolding software
Fig 2
Contact probability and strategies used to evaluate distance between scaffolds adopted by different software.
a, Ideally, the distribution of Hi-C contact is 1/x. Heat map shows the diagonal position of interaction density is very high, the farther away from the diagonal, the lower the interaction density becomes. b, Heat map shows the chr2 [0–35MB] assembled by LACHESIS, where c1, c2, c3 and c4 represent scaffolds and the rectangle represents the number of Hi-C reads links with two scaffolds. Compartment and TADs produce many long-range interactions with densities higher than adjacent interaction densities. c, Strategy to evaluate distance as adopted by LACHESIS and ALLHiC. d, Strategy to evaluate distance as adopted by 3D DNA. e, Strategy to evaluate distance as adopted by SALSA2. f, Strategy to evaluate distance as adopted by Puzzle Hi-C. g, CV of interaction density with the triangle region and square region. h, Errors of the distance between two scaffolds with different gap sizes in Puzzle Hi-C. i, Errors of different strategies to evaluate the distance between two scaffolds with 1000 samplings.