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I'm trying to visualize one of our E5 genomes (`Apulcra-genome.fa`) in IGV, but I can only view individual chromosomes at a time. When I click the "view whole genome" button I just get directed to vie…
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# Goals
- [ ] Remove an entire genome and all associated indexes in a single action (Data Manager created or not)
- [ ] Remove a specific index or set of indexes associated with a specific tool (Dat…
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Is there a way to increase the visibility of SNPs at wider views? In the example below, I can see SNP differences between alignments in a 56 kb window, but not in a 140 kb window, which encompasses th…
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### Setup
I am reporting a problem with Biopython version, Python version, and operating
system as follows:
3.8.10 (default, Nov 22 2023, 10:22:35)
CPython
Linux-6.0.12-76060012-generic-x86_6…
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**Describe the bug.**
The print statement of each species' fitness value after each generation is slightly incorrect. In the following, I am referring to the source code of the Population-class (http…
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Hi,
I am classifying Phages according to their taxonomy. I am having the issue that my fast afiles have fractions of the genome instead of the whole genome:
My fasta files have the format
Geno…
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> The abundance value is simmilar to TPM in RNAseq. It represents the average read coverage of a bin per million reads. So its really a standardized read coverage estimation.
>
> Salm…
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Some of the CRISPR locus start and end positions reported in the CRISPR db results are apparently wrong. This affects a small number of organisms and I noticed it when I saw that in these cases, all s…
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### Operating System
Ubuntu 22.04
### Other Linux
_No response_
### Workflow Version
v1.4.0
### Workflow Execution
Command line (Cluster)
### Other workflow execution
_No re…
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as of the merge of #160, charcoal now performs the following steps -
1. find candidate genomes for contamination analysis, based on sourmash shared hashes with GTDB r95
2. download genomes and per…