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jaleezyy / covid-19-signal

Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.
MIT License
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Version 2 for long-reads #45

Open fmaguire opened 4 years ago

fmaguire commented 4 years ago

Bigger milestone to start as separate repo but version of pipeline to support minion and pacbio with test data for both

jaleezyy commented 4 years ago

I can always make that repo whenever. :)

fmaguire commented 4 years ago

As soon as we have data, make that repo, and we can close this stub issue!

jts commented 4 years ago

I strongly recommend that if you add support for MinION data you only wrap the artic commands from the SOP in the same style as the nextflow wrapper. There's been a lot of work to get primer trimming right for nanopore data and handling the two amplicon pools correctly and it would be challenging to start from scratch

fmaguire commented 4 years ago

Yeah, that is pretty much what were thinking for the core components @jts definitely don't want to reinvent the wheel.

passdan commented 3 years ago

Was wondering if you did any more on supporting nanopore through the signal pipeline? We've been using the pipeline for illumina (works great!) and wanted to touch some nanopore.

As far as I can see there's not an option but wanted to check if there was before I jump ship to the artic nextflow for doing the nanopore data. Thanks!

jaleezyy commented 3 years ago

At present, we don't have a version for Nanopore. The ARTIC Nextflow pipeline really goes a long way for long-read sequencing.

Glad SIGNAL has been of use!