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I see you now have PromethION data for several of the individuals, available in fastq format. However, I don't see a link to the raw fast5. Is this available somewhere?
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This issue ticket is for a task note. Rename the current input parameter `data_type` ("HIFI"/"ONT") to `seq_data_type`. Because we want to add a new input parameter `genome_data_type`.
* `seq_data_…
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Hi!
I ran the standard_haploid_qc workflow and saw that it was using a really old version of minimap2 in the asmgene call.
The asmgene task (here: https://github.com/human-pangenomics/hpp_produ…
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We could upload the different VCFs produced by vg and the other methods benchmarked. Maybe also the graphs for the different datasets, human and yeast?
I've asked Miten to see if we can use the pub…
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Hi,
Thank you for this fantastic resource!
The CAT genes index does not appear to have annotation entries for 3 samples:
HG002
HG005
NA19240
https://github.com/human-pangenomics/HPP_Year…
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1) Setup section has the Metagenomics lesson information, not the Pangenomics
2) For a local installation I would suggest providing the yaml files for the environments, instead of the individual inst…
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[Manuscript](https://www.overleaf.com/3825469397tfcwhwsqmdpb#2ce1dd)
[Response to reviewers](
https://docs.google.com/document/d/1m4l7jghF3607_i27EFCB5CH8l_q3dIUbq2Cw3U7auCg/edit)
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Hi there @anialisiecka,
I am applying ALIBI to a chr20 human pangenome graph https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/scratch/2021_11_16_pggb_wgg.88/chroms/chr20.pan.fa.a2fb2…
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In addition to artifacts and programs, the anvi'o docs now supports workflows following the PR #1977.
Adding a new workflow is quite straightforward, and every file that needs to be edited to add a…
meren updated
9 months ago
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Hi vcflib developer,
Thank you all for offering such a multi-purpose tool. However, I recently faced a problem that seems because vcflib doesn't support csi index of vcf.
As [this issue](https:…