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I noticed that a lot of memory is used when `link_clusters.pl` is run in parallel. Can you explain what would determine the memory usage for each execution of this script? Depending on the response, …
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Hi, the software seems very good, but I am new in metagenome analysis and I have questions about the selection of appropriate reference genomes (indexes) when using 'hostile'.
1.
I read the "Refe…
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hello,
i am screening the minion generated sequences of bacterial genome and getting these results. even after geeting killed the sequences are showing hits on these genomes. is it running properly?…
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Hi again!
Just thinking about the RefSeq versus GenBank question for analysis of a metagenome (containment). Aware that Sourmash may struggle with similar genomes (ie strains) due to a smaller numb…
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Dear all,
I am running **SynTracker v1.3.0** on a haploid fungal reference genome with the default parameters.
For many of the .tab BLAST output files I get an error message, that it contains **…
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Hi Diener,
would it possible to provide detailed description on the procedures that generated those GEM reference database? I found it quite useful while I am hesitating to use it in my manuscript wi…
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Hi,
I am trying to run sRNARFTarget with a group of sRNA's against bacterial genomes. I am running into an issue with the initial command: nextflow run sRNARFTarget.nf --s sRNA.fasta --m mRNA.fast…
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# Genomic context aka neighborhood analyses
- [ ] `edirect` and `eutils` to fetch genes of interest (from a list)
- [ ] + slurm
- [ ] user-input: no. of neighbors on each side (default: ±7)
- […
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### Operating System
macOS
### Other Linux
_No response_
### Workflow Version
v1.2.0
### Workflow Execution
EPI2ME Desktop application
### EPI2ME Version
v5.1.14
### CLI command run
_No res…
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Hi Bakta developers!
Thank you for a great tool for plasmid and bacterial genome annotation!
I am using Bakta specifically to annotate the origin of replication. In some of my plasmid genomes, Ba…