[FEATURE REQUESTS] - post here for suggestions/feature requests

[bluenote-1577]

Feature requests

Purpose: this is a place to easily log suggestions/feature requests. E.g:

• "I want to display XXX output as an option!"
• "I want to be able to combine database sketches!"

Give a rationale and provide concise/clear instructions if possible. Opinions are welcome too.

You're welcome to email me or open another issue. This thread is to aggregate suggestions without the hassle of opening another issue.

Current feature requests

Here are some current feature requests.

Originally posted by @jolespin in bluenote-1577/skani#23 (comment)

• Option for renaming samples. Sylph currently fixes each sample sketch to the read names. ` done in v0.5.0
• Command line options for inspecting database sketches.
• Command line option to append/merge databases.
• Line-delimited file for database sketches for sylph profile/query done in v0.5.0

@fplaza #6 (comment)

• Save read length while sketching so the user does not have to provide it to compute true coverage. done in v0.5.0

#7

• Different ways of sketching reads and groupings

[fplazaonate]

Hi Jim,
Here is a suggestion:
Save read length while sketching so the user does not have to provide it to compute true coverage.

[astrovsky01]

Is there/could there be a method to output unassigned reads into a file as an output?

[bluenote-1577]

Hi @astrovsky01,

This is unfortunately not possible due to the way sylph works. It doesn't classify each read. It operates on the ensemble of reads. This means it can not output unassigned reads, only estimate the percentage of.

[jolespin]

@bluenote-1577 I'm not sure how the backend algorithm works but is it possible to add Align_fraction_ref to Sylph output similar to Skani? Would be useful to know how much of the genomes being profiled are covered.

[bluenote-1577]

@jolespin Hi Josh, unfortunately this isn't possible. This is because skani actually tries to get a pseudo-ish alignment, by sylph doesn't do anything like that. I agree it would be very nice if it were possible though...

[jolespin]

Ok that's good to know! Would finding the overlap in kmers do the trick or is it way more complicated than that?

[jolespin]

Also one more question, does sylph allow for outputting abundance instead of relative abundance?

[bluenote-1577]

@jolespin sorry for the late response:

1. There may be something that could be done for pseudo-alignment overlapping k-mers ... but it's a very nontrivial algorithmic thing :)

2. What do you mean by abundance instead of relative abundance? Sylph outputs coverage (Est_cov) if that's what could be helpful

[jolespin]

There may be something that could be done for pseudo-alignment overlapping k-mers ... but it's a very nontrivial algorithmic thing :)

I can imagine that is quite complicated. Themisto just popped up on my radar so I'm going to give this a try soon.

What do you mean by abundance instead of relative abundance? Sylph outputs coverage (Est_cov) if that's what could be helpful

Is the Est_cov what you use before normalizing the Taxonomic abundance?

Taxonomic_abundance: normalized taxonomic abundance as a percentage. Coverage-normalized - same as MetaPhlAn abundance
https://github.com/bluenote-1577/sylph/wiki/Output-format

I'm mostly curious on how some of my compositionally valid network analysis (https://github.com/jolespin/ensemble_networkx) differs between coverage normalized and unnormalized data but definitely not a critical assessment. Just a bit of curiosity.