Which contigs each sscaffold contains after running run-asm-pipeline.sh.

[苏摩]

Hello;

    When I finish running the 3d-dna pipline, how do I know the number of contigs contained in each scaffold.

best;

GaoHong Xiao

[Olga Dudchenko]

You can parse the assembly file. There is a slide somewhere on the forum explaning the format, but briefly, the second part of the assembly file (part w/o > at the beginning of the line) will have one line for each scaffold, and each line with have numbers separated by spaces. Each number represents a piece of the original sequence (contigs if you started with contigs). If you just want to run the stats to calculate how many contigs there are you can use some of the existing tools or the 3d-dna/supp/n50 tool. Best, -Olga