Details about the --reference parameter

[gallardoalba]

Dear Dr. Woodcroft,
We are working in order to include CoverM in Galaxy, and it would be great if you could clarify a few doubts that we have. Could you provide us with some additional details about the cases in which is strictly necessary to use the --reference parameter? Under my understanding, it is only strictly required when providing metagenomic assemblies. Also, it would be great if you could clarify this sentence:

However, while not necessary, --reference can be specified if an alternate reference sequence set is desired.

Thank you so much for your attention.

[wwood]

Oh good to hear. To clarify you are talking specifically about the genome subcommand? I'm not quite sure what "when providing metagenomic assemblies" means. For genome mode, --reference is only required when the sequences cannot be derived from the input genomes definition e.g. it cannot be derived when specifying --genome-definition. The user can optionally use --reference to specify a set of sequences that differs from simply concatenating the genomic sequences. I can see how the help message is a little confusing there - does the above clear it up? If so I can modify the help message accordingly. Thanks.

[gallardoalba]

Thank you so much for your response. Yes, I am referring to the genome subcommand. So, in order to illustrate it, we could use a de-novo genome assembly as input for --genome-fasta-files, and a reference genome of the same genome as input for --reference. Is it correct?

Regards

[wwood]

You could do that, but it would be equivalent to not specifying --reference at all. So why bother? -\------------- Ben Woodcroft Group leader, Centre for Microbiome Research, QUT

…

________________________________ From: Cristóbal Gallardo ***@***.***> Sent: Wednesday, April 20, 2022 9:39:10 PM To: wwood/CoverM ***@***.***> Cc: Ben J Woodcroft ***@***.***>; Comment ***@***.***> Subject: Re: [wwood/CoverM] Details about the --reference parameter (Issue #111) Thank you so much for your response. Yes, I am referring to the genome subcommand. So, in order to illustrate it, we could use a de-novo genome assembly as input for --genome-fasta-files, and a reference genome of the same genome as input for --reference. Is it correct? Regards ― Reply to this email directly, view it on GitHub<#111 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAADX5EA4B2P72QDPE4535DVF7UF5ANCNFSM5T3PG75Q>. You are receiving this because you commented.Message ID: ***@***.***>

[gallardoalba]

Thanks!