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Hi,
I am new to using Github codes to run the pangenome analysis. I am using more than 50 genomes to do this and some of the genomes are from JGI and hence I have .gff and .fna files. Most of my geno…
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Hi all, I'm noticing a performance problem with hmmscan run on some simple bacterial genomic protein sets. With one thread it does fine. But even when given independent processes on independent thread…
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I think I must be doing something wrong.
I created a meryl db using the paired reads from an Illumina run and then ran Merqury as described and I'm getting a quality value of +inf. Do you have any …
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This has been commented on in several lineage requests, but probably deserves its own issue.
From footnote to Table 13 of https://assets.publishing.service.gov.uk/government/uploads/system/uploads/…
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Hi,
I pulled the latest docker image, but am struggling with the Documentation. What I am trying to do is create a Metagenomics sample of multiple genomes, with a mixed abundance. The genomes thems…
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I am getting started with using NPLinker (using the docker image) so after completing the 'tutorial' using the example dataset, I tried to load the Crüsemann dataset (MSV000078836) from PoDP. However …
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Dear atlas developers/users,
I have generated a gene catalog using atlas. Do you have any guidline how to map back and quantify the proportion of genes (I guess noramlizing by gene length) in the d…
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by Anderson Brito
Description: Sub-lineages and new designations within P.1, and some issues related to existing sub-lineages.
Sub-lineage of: P.1
**Proposed lineage name**: P.1.13
Earliest …
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Hello,
I've generate a large HAL file using cactus v1.3.0.
Is there a way to query the HAL archive for specific positions in one genome and get the aligned base or bases in a second genome using py…
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Invocation looks like following:
```
(atlas) animeshs@DMED7596:~/ayu$ atlas run all
[2021-06-19 12:08 INFO] Executing: snakemake --snakefile /home/animeshs/miniconda3/envs/atlas/lib/python3.6/sit…