Can minCoverage threshold (default 10x) be changed by the user and question about --completeness

[tpshea2]

From the paper I see "We classify a contig as high-coverage if its coverage by reads exceeds the minCoverage threshold (default value 10x), and low-coverage, otherwise.". Is there a way for the user to change this minCoverage threshold? I have somewhat lower yield of PacBio for some human stool samples and would like to lower the minCoverage value from 10x to about 5x. I see that the viralFlye.py parameters has only --min_viral_length --completeness parameters. Also I see that viralFlye.py completeness parameter is set to 0.5 ( "Completeness cutoff for viralComplete, default - 0.5" ) however when I run the usage for viralcomplete it indicates a default of 0.9 " -thr THR Completeness threshold (0.0-1.0), default = 0.9". Are these two different thresholds or do they refer to the same threshold and it is just the case that one of the two values is reported incorrectly in the usage? Thank you for your help.

[skchronicles]

@Dmitry-Antipov I am running into a similar problem with nanopore data. I was just wondering what are your thoughts on this issue.

[Dmitry-Antipov]

Hi,

For the completeness - paper is correct, default used by viralFlye is different with default by viralComplete - we decided to weaken the requirement. This can be changed by providing different fraction for --completeness command line option.

For the coverage you can change constants cov_thr in extract_components_from_gfa.py and mincov in extract_circulars_metaflye.py after cloning but prior running install.sh