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Would it be okay to switch:
https://github.com/KwanLab/Autometa/blob/0d9028cf7bad20d6e28667aaba9d3889a15ace09/autometa/common/kmers.py#L601-L607
to adapt to a lower pca dimension when there aren…
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Hi ！@Puumanamana
run pipeline :
coconet run \
--fasta R63.contigs.fa \
--bam R63_sort.bam \
--output coconet_binning_results \
--threads 16
# err report:
00:…
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Dear Authors. Could you clarify please.
Is there a stronger threshold for the identification of eukaryotic viruses? Because those contigs, which according to the program belong to eukaryotic viruses …
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* pharokka version: 1.7.3
* Python version: 3.10
* Operating System: Linux
### Description
I ran the command as below
`pharokka.py -i 5_redundant/${line} -o 6_pharokka/${sample} -t 1 -f -d /bee…
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Hello,
I ran the tool on a FASTA file representing a genome which contains many different contigs. I used `python Promotech-master/promotech.py -g -i results/ -o results/` to generate the final res…
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Due to differences inc ommand line parameters, I assume `fastq` is actually for short sequence reads, and `fasta` for contigs?
What if my reads are in FASTA format? Will `fastq` barf ?
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Hello, thank you for providing this excellent tool. I would like to perform ARGs analysis for contigs, how can I download the SARG v3.0-L database? The link https://smile.hku.hk/ARGs/Indexing only h…
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Thanks for maintaining this great software! I'm having an issue with easy-taxonomy using GTDB (but not NCBI with the same query input), described below. Using a conda install of version 15.6f452.
…
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When 2 contigs overlap and the ratio of that matching region is < 10% Ray won't merge those 2 contigs.
Exemple :
```
Overlap=9142/9142 (100%)
```
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Hi,
I am running v1.2.2. I wonder why Savana would spawn out more threads than I specified with `--threads`?
I am trying to reduce the memory footprint at the expense of running time by using fewe…