andersen-lab / hcov-19-genomics Goto Github PK

I'm trying to pull all of the consensus genomes, but it takes forever to git clone or to download a zip file of the repo because of the large number of files. I understand the desire to have each consensus sequence in a separate file for the sake of git push friendliness (as well as to circumvent GitHub's file size limit), but would it be possible to add a GitHub Action to automatically create a new "Release" that includes a concatenated single-file FASTA attached to it upon every new commit?

As an example, the GitHub repo I use to track/store the LaTeX source of my CV has a GitHub Action that creates a new release, compiles the LaTeX source to PDF, and attaches the PDF to the release upon every single push:

https://github.com/niemasd/curriculum-vitae

The file that defines the GitHub Action can be found here:

https://github.com/niemasd/curriculum-vitae/blob/master/.github/workflows/compile.yml

I think you would just need to replace LaTeX Compilation step with a step that just runs cat consensus_sequences/*.fasta > consensus_sequences.fasta (or, ideally, cat consensus_sequences/*.fasta | gzip -9 > consensus_sequences.fasta.gz to compress), and then just edit the Publish Release step to point to your consensus_sequences.fasta.gz file

I'm happy to help if desired!

Generate final output readme for inspection automatically. Will need to incorporate resolving of county names, but this should be trivial given small number and regularity.

Hi there,
As you mentioned the Illumina data here were processed with iVar, I wonder if the iSNVs and insertions/deletions data (vcf?) are available? Thank you very much.

just as an FYI... export coalesces the sample names in the middle to ... in the substitution .csv and truncates the list in the deletion one before the list is complete.

NBD, just letting you know @AlaaALatif.

https://github.com/andersen-lab/HCoV-19-Genomics/tree/master/variants

Integrate biosample id mapping into metadata file based on uploads, and additionally add status ids to identify when these sequences, bam files, and metadata have been uploaded

I noticed that the consensus_sequences.fasta.gz files that are automatically created and attached are broken: they seem to just be empty files that were then gzipped (so they're 20 bytes overall). The last functional release seems to have been SequenceUpload_2022.11.22_04-01, and then it was broken in SequenceUpload_2022.12.03_01-21

Hi

Thanks for providing the data.
I was trying to reproduce consensus from your bam file but don't know primers position for trimming. Could you please share bed file or fasta primers?

Thanks