When we use long-read assemblies, we can be tempted to consider each contig as a MAG/genome, especially if you filter for a high min contig size. To get quick info on these putative genomes, I usually create a fake collection where each contig has its own bin. It is not very hard to do, but I realize that we already have a script command which does something very similar: anvi-script-add-default-collection.
This command create a default collection of one bin for all contigs (when your contigs correspond to one genome and you know it).
I suggest we add a parameter in this command to create a default collection with as many bins as contigs.
The solution
An option like --collection-type with either "everything" (could be default) and "each". Or something like that.
Beneficiaries
Mostly people working with long-read assemblies. So more and more people.
meren
commented
1 year ago
The need
When we use long-read assemblies, we can be tempted to consider each contig as a MAG/genome, especially if you filter for a high min contig size. To get quick info on these putative genomes, I usually create a fake collection where each contig has its own bin. It is not very hard to do, but I realize that we already have a script command which does something very similar: anvi-script-add-default-collection.
This command create a default collection of one bin for all contigs (when your contigs correspond to one genome and you know it).
I suggest we add a parameter in this command to create a default collection with as many bins as contigs.
The solution
An option like
--collection-typewith either "everything" (could be default) and "each". Or something like that.Beneficiaries
Mostly people working with long-read assemblies. So more and more people.