Graph construction

We expose two optional parameters that greatly influence the way the fragments, and subsequently the assembly graph, gets constructed.

The -w/--wordsize parameter allows you to set the fixed $ k$-mer length used during fragment construction. If left out, the assembler tries to estimate a reasonable word size $ k$ based on the number of bases in the input data.

The -c/--min-coverage parameter specifies a lower bound on the number of times, we want to see any given $ k$-mer for it to play a part in fragment construction (default 3).

Should you want to inspect the resulting fragments, you can choose to save them to a FASTA file using the -f/--savefragments parameter.

You also have the option of saving the constructed graph using the --savegraph parameter. That way you can experiment with different post-processing steps without continuously rebuilding the graph. Afterwards, you simply reuse the graph by adding the --loadgraph parameter in subsequent runs.