mag
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nf-core
Enter at postbinning stage
Description of feature
Decided I wanted to try and bin my data using Vamb, which isn't in the pipeline yet. Would be a useful feature to be able to supply a csv (or directory?) of bins and jump directly into the bin QC/taxonomy/annotation steps!
Might try my hand at this one if I find a bit of time, but I suspect that it will be finnicky depending on what exact metadata we will want to tag onto the input bins and that might need some discussion.
You can try, but tbh it likely would be faster to just add vamb to the pipeline 🤣🤣🤣
Having looked at Vamb, as it (ideally) require concatenating all assemblies and renaming contigs along a complicated scheme - I think it's going to play havoc with any system that's comparing bins using contig names (DAS_Tool and Tiara)... 😅
I guess we will need to make a metadata file to track them or something and covert headers back?
"Concatenate the FASTA files together while making sure all contig headers stay unique"
If that's all it's doing, might be a reasonable thing to do upstream immediately after assembly anyway thinking about it...
Furthermore, if you want to use binsplitting (and you should!), your contig headers must be of the format {Samplename}{Separator}{X}, such that the part of the string before the first occurrence of {Separator} gives a name of the sample it originated from. For example, you could call contig number 115 from sample number 9 "S9C115", where "S9" would be {Samplename}, "C" is {Separator} and "115" is {X}.
So it's a little more complicated! I'm not sure if renaming all the contigs initially is the best solution disk-space wise - as we just create a copy of all assemblies with different headers for a tool that we (potentially) might not choose to run...
Not to mention mapping the reads to the concatenated assembly, and then parsing that separately through the depths workflow 🫢
Furthermore, if you want to use binsplitting (and you should!), your contig headers must be of the format {Samplename}{Separator}{X}, such that the part of the string before the first occurrence of {Separator} gives a name of the sample it originated from. For example, you could call contig number 115 from sample number 9 "S9C115", where "S9" would be {Samplename}, "C" is {Separator} and "115" is {X}.
So it's a little more complicated! I'm not sure if renaming all the contigs initially is the best solution disk-space wise - as we just create a copy of all assemblies with different headers for a tool that we (potentially) might not choose to run...
Not to mention mapping the reads to the concatenated assembly, and then parsing that separately through the depths workflow 🫢
Ugh ok.
It's weird though as earlier the documentation implies you don't have to do all of that?
I don't have a good suggestion then 😅, sounds like it'll all be painful one way or another...
As a stopgap measure, I've written mgenotatte to do just that: genome QC, dereplication, and taxonomic annotation https://github.com/maxibor/mgenottate
As a stopgap measure, I've written mgenotatte to do just that: genome QC, dereplication, and taxonomic annotation https://github.com/maxibor/mgenottate
Ah, that's cool! In the end I just ended up forking mag, deleting the first part of the main workflow and dropping bins in via directory input: https://github.com/prototaxites/mag/tree/bin_entry
Also, I have a separate pipeline for metagenome gene annotation that is just a couple of characters different in name from yours: https://github.com/prototaxites/mgannotate 😅