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**1. What were you trying to do?**
Running vg autoindex on yeast assembly together with known variants from ensembl:
```
vg autoindex -t 2 --workflow giraffe -r resources/genome.dna.saccharomyc…
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I'm trying to load the HPRC PGGB-generated GFAs from here: https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=pangenomes/freeze/freeze1/pggb/chroms/
I get this error message:
`…
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Hi there,
Thanks for the cool software/preprint.
I'm wondering if there are good parameters for remapping nanopore reads, say error rates between 90-95% and lengths between 10 - 100kb? I see tha…
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hello,
i tried to build a themisto index with this command:
themisto build -k 31 -m 100000 --input-file data.fa --index-prefix data_index --temp-dir tmp --n-threads 32
and the software retu…
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Hello,
**What I have done**
1) Used `ppgb` to build a graph genome with the `-v` parameter to directly use `vg deconstruct` in the pipeline, to generate a .vcf file
2) Used `vcfbub` to avoid…
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Is there a publicly available file that tells the lengths of the chromosomes? I've not seen one listed on UCSC's site (https://t2t.gi.ucsc.edu/chm13/hub/t2t-chm13-v2.0/) nor on the list of resources o…
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## The need
The slumbering behemoth known as `Genome View` currently lies dormant, its genome clustering abilities waiting silently in the wings. Meanwhile, rumblings from the current Anvio user ba…
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Hello,
The GFF version 2.0 seems to be lacking mitochondrial encoded genes. Will you be releasing a new annotation including those?
Alternatively, would it be safe to assume that the coordinate…
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The annotations available here: https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/CHM13/assemblies/annotation/chm13.draft_v1.1.gene_annotation.v4.gff3.gz appear to be version 1.1 and do not con…
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## Solution
The problem is due to a bug in HMMER `v3.3.1`. If you downgrade it the following way, the error will be resolved:
```
conda install -c bioconda hmmer=3.2.1
```
## Short descript…