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epi2me-labs / wf-clone-validation

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sequence alignment with "full reference QC"? #53

Open ChristopherRichie opened 1 month ago

ChristopherRichie commented 1 month ago

Ask away!

When i run v1.3.1 without providing a reference, I see a "multiple sequence alignment" (MSA) even if there is only one plasmid in the "group".

When i run v1.3.1 and provide a full reference (or an insert reference), I get "full reference QC" (or "Insert variants") that indicates Indels and SNPs were found, and a BCF file.

is it possible to specify a pair-wise alignment (final.fasta vs full_reference/insert_reference) as an output in the report? The BCF file is not as immediately useful for my small plasmids, where i just want to know if the gene of interest has a mutation or if there is a deletion in my plasmid.

thanks

sarahjeeeze commented 1 month ago

Hi, thanks for the feedback,

For the first one - we will update this so it doesn't output single sequence MSA's, good point. For the second one - yes, I think a pairwise alignment would be best. We currently are outputting an aligned BAM and in the future hope to display this in the IGV embedded with the application - are you running it in the app? Or would it be useful to have this as a section in the report?