-draft option abundance file

[BeckyGenomics]

Hello, firstly I would like to thank you for creating InsilicoSeq!

Secondly, I am using multi-config draft genomes to generate a simulated metagenome.

I was wondering if there is any option to use an abundance file with draft genomes? Just as there is with the -genomes flag? Does it also default to lognormal abundance if not specified?

Many thanks,
Becky

[HadrienG]

Hi!

--draft is not currently compatible with abundance files and default to log-normal abundance.
There'd be no technical difficulty in implementing abundance files for draft genomes, but I'm still unsure what the best design would be.

For whole genomes (with the --genomes option the abundance files has to contain the ID of the sequence in the fasta file, which is not possible for drafts since we have more than one sequence per file that need to have the same abundance.

What I could imagine is that the abundance file would accept a file name for draft genomes. As an example:

genome_a 0.1
genome_b 0.4
path/to/draft_a.fasta 0.2
path/to/draft_b.fasta 0.3

But as I said I haven't quite made up my mind yet. As a user do you think you'd be fine with mixing genome IDs and paths in the abundance file?

Best,
Hadrien

[bioinfoMMS]

Hi Hadrien,
Thank you for this great tool! I also would like to be able to specify abundances for draft genomes. As a user, I would be fine mixing genome IDs/names with file names (as long as it was clear in the documentation that this is what one needs to do).
Thanks,
Maddy

[novitch]

Hi Adrien,
In order to show you that it can be interesting, I was looking for the same option. No problem to mix pathway for draft and genomeID.

Thanks for your tools,
Cheers,
Alban.

[HadrienG]

Thanks for the feedback folks. I'll look into if for the next minor release.

[apcamargo]

Given that the amount of fragmented genomes is increasing really fast due to the popularization of MAGs, I think this feature would be really useful!

Mixing genome IDs and paths seems to be a good solution. I don't see a problem with it.

[HadrienG]

Planning this for 1.5.0, which should be out before the end of June :)

EDIT: better late than never, but 1.5.0 is out

[novitch]

:), Thanks, will use it on my next benchmark !

[apcamargo]

That's great! Thanks @HadrienG!