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https://mp.weixin.qq.com/s/hYfXZ0iBCUrHIwVvWv-a1A
ixxmu updated
3 years ago
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## Short description of the problem
anvi-get-sequences-for-gene-calls behaves different than expected and doesn't export DNA sequences for gene calls from genome_storage.db
## anvi'o version
…
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Given [`cov0r.fa`](https://serratus-public.s3-us-west-2.amazonaws.com/seq/cov0/cov0r.fa), and an incoming stream of aligned reads (BAM format), count the total number of reads that match per sequence.…
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Our online documentation is falling behind. I see multiple critical needs there. Note: All these updates should be submitted to [this](https://github.com/merenlab/web/tree/anvio-v6) branch of our web …
meren updated
3 years ago
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## Short description of the problem
Dear anvio team, @ivagljiva and @meren,
I'm trying to play with your new estimate-metabolism functionality, and in order to do so setup kegg kofams. However, …
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Hi,
thanks a lot for this wonderful potential replacement for Roary which is not actively maintained anymore.
Would it be possible to create a core genome alignment just like Roary does (`core_gen…
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Does panaroo produce a core alignment file similar to Roary? Or is my output missing it?
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I am trying to construct a pan genome using genomes that consist only of contigs. However, pirate gives me the following error
```
- running mcl on pan_sequences at 50
- 0 clusters at 50 % - …
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Hi,
I have a few questions regarding the improving of the layout with a ref genome:
using:
python ~/repos/panaroo/scripts/reference_based_layout.py 0 final_graph.gml capacity_cut_edges.txt --add…
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Hi!
Odd little problem. For some reason when I run `anvi-estimate-metabolism --external-genomes external-genomes.txt -O output.txt --kegg-data-dir /PATH/to/DB` I get an error. See below for the er…