Commands

To call a command:

ctx31 <command> <options>

Available commands are:

Command     |                Explanation

----------------|--------------------------------------------- build | build a cortex graph (.ctx) view | view and check a cortex graph file (.ctx) check | load and check graph (.ctx) and path (.ctp) files clean | clean errors from a graph join | combine graphs, filter graph intersections supernodes | pull out supernodes subgraph | filter a subgraph using seed kmers reads | filter reads against a graph extend | extend contigs using a graph contigs | pull out contigs for a sample inferedges | infer graph edges before calling thread thread | thread reads through cleaned population pview | view read threading information pmerge | merge path files (.ctp) call | call variants unique | remove duplicated bubbles, produce VCF place | place variants and genotype