After ran “preprocess”, “correct”, "filter", "overlap" and “assemble” with default settings, I got two contigs files for reference genome ref_contigs.fa and query genome query_contigs.fa. When I tried to run "graph-diff" with the following command to call the variants,
Usage: sga graph-diff [OPTION] --base BASE.fa --variant VARIANT.fa --ref REFERENCE.fa
Find and report strings only present in the graph of VARIANT when compared to BASE_
I tried all possible commands, but they didn't work. I installed SGA by conda.
Could you tell me what's wrong with the command?
Hello Jared,
After ran “preprocess”, “correct”, "filter", "overlap" and “assemble” with default settings, I got two contigs files for reference genome ref_contigs.fa and query genome query_contigs.fa. When I tried to run "graph-diff" with the following command to call the variants,
_sga graph-diff -p D0D3 -t 16 -k 61 -x 10 --variant query_contigs.fa --ref refcontigs.fa
it kept reporting wrong message:
_Error: unrecognized algorithm string:
Usage: sga graph-diff [OPTION] --base BASE.fa --variant VARIANT.fa --ref REFERENCE.fa Find and report strings only present in the graph of VARIANT when compared to BASE_
I tried all possible commands, but they didn't work. I installed SGA by conda. Could you tell me what's wrong with the command?
Thanks a lot, Ming