Coverage parameter?

[Anto007]

This looks like an interesting tool and I'm looking forward to testing it out. Before going ahead with the testing, I was just curious if your tool has a coverage cutoff parameter too, for example query coverage or query/hit coverage?

[NuruddinKhoiry]

Hi Jubin

I am really sorry for my late reply. I had many exams a few days ago.

I appreciate your interest in testing this tool.
Unfortunately, I haven't included the query/hit coverage parameter in the mining algorithm. However, you can still add it when you run the blastn program.

For example:
In the "full_pipeline" mode, you can use -bp option and specify the query/hit coverage. e.g., -bp "-qcov_hsp_perc 80"

$blastMining full_pipeline
-i ASV.fasta
-o vote_pipe
-bp "-db nt -max_target_seqs 10 -num_threads 5 -qcov_hsp_perc 80"
-m vote
-e 0.001
-txl 99,97,95,90,85,80,75
-n 10
-sm 'Sample'
-j 8
-p lca_method
-kp
-rm

Best regards
Khoiri

[Anto007]

No worries @NuruddinKhoiry and many thanks for your response. Sure, I can just stick to the coverage parameter in blastn