Enter the pipeline at step 3 (detect and remove chimeric reads)

[reginabohnert]

Description of feature

When already having CCS consensus reads cleaned from primer sequences and no raw subreads, it would be very helpful to have an option to enter the pipeline at step 3 (detect and remove chimeric reads).

[sguizard]

Hi @reginabohnert,

It's a good idea, it would avoid a lot of computation.
I also have in mind the possibility to enter at mapping step.
Adding this option imply to have an alternative input file format.
I need to check how it could be implemented in order to comply with the guidelines.
I'm pretty busy for a moment, but I'll try to have a look in the coming weeks.

[reginabohnert]

Hi @sguizard,

Many thanks, it would be very helpful. Looking forward seeing it implemented!

[cazzlewazzle89]

Hi @sguizard
Just checking in to see whether you were able to implement this? It would be a very handy feature.
Thanks, Calum

[sguizard]

Hi @cazzlewazzle89,
I have been thinking about this feature since the announcement of the new Pacbio sequencers.
Since they will not produce the subreads and directly send the HiFi generated with deepconsensus, this pipeline will become obsolete at some point.
That why I'm thinking to forking it (tamannot?) and make more generic by chopping down the isoseq part.
The pipeline would take as input a fasta and an optional gff.
I also have to see if this new pipeline should (and is allowed to) seats on nf-core repo or I keep it personal.
Once I found a new contract, I'll work on this.

[vicenciooostra]

Hi @sguizard,
this sounds like a great feature; I'm in the same boat, have my HiFi reads and would like to enter the pipeline after the isoseq3 step. Do you think this will be implemented?
Best regards, Vicencio

[sguizard]

Implemented!