FAQ

Frequently asked questions

1. The sga assemble/fm-merge steps are taking too much time/memory.

   The cause of this problem is usually selecting an overlap length that is too short. If the overlap length is very short, many edges will be created in the graph between reads that have short repeats at their ends. The suggested parameters for 100bp reads are overlap length 65 for fm-merge and overlap length 75 for sga assemble. You should try this parameter combination first, then tweak the overlap parameter in sga assemble to try to improve the assembly.

2. The genome I want to assemble has high heterozygosity.

   The default parameters for sga assemble are very conservative and will not aggressively remove variation from the string graph. You should tweak the parameters listed in the "Variation removal" section of sga assemble --help