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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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Run ncov-tools pipeline on output #43

Closed fmaguire closed 4 years ago

fmaguire commented 4 years ago

Add pipeline support for running https://github.com/jts/ncov-tools

Issue created at ncov-tools repo: https://github.com/jts/ncov-tools/issues/2

jaleezyy commented 4 years ago

Maybe add to Snakemake postprocess protocol?

agmcarthur commented 4 years ago

Extra bonus of using ncov-tools is ability to generate multiple sequence alignments that also include GISAID data, but can we ask @jts to add masking of http://virological.org/t/issues-with-sars-cov-2-sequencing-data/473

agmcarthur commented 4 years ago

The amplicon coverage figure compress the results of all samples into a single image, making resolution poor. Any chance of also generating a separate image for each sample?

jts commented 4 years ago

The latest version of ncov-tools will put 8 coverage plots per page, so hopefully that will look a bit better now?

agmcarthur commented 4 years ago

@nknox can you see if the 8 coverage plots per page works better for PHAC? Thanks.

fmaguire commented 4 years ago

Working on this: plan is to add as a submodule (so recursive git clone of repo will clone) and then modifying @kmsmith137 post-processing script to prepare and run files through the pipeline.

Currently having issues with the included env not solving but will see if I can work out what the issue is tomorrow.

nknox commented 4 years ago

@nknox can you see if the 8 coverage plots per page works better for PHAC? Thanks.

Yes looks better now!