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Hello,
I've been trying unsuccessfully to build a custom Ganon (v2.1.0) database, however, I am running out of memory on the raptor prepare stage on a machine with 512GB RAM. I have tried to build …
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Hi,
I have tried run the command `kraken2 --db=~/Metagenomics/kraken/krakenDB --threads 20 database.kraken`
However I am getting the error message:
kraken2: database ("~/Metagenomics/kraken/…
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Thank you for this wonderful tool!
Should we filter out the host (human) genome before executing the pipeline e.g. using kneadData or fastp? the same also applies to the PhiX genomes?
I tried He…
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I am considering looking for overlapping genes in some viral metagenomes I obtained. I am not interested into the overlaps themselves but more into genes that I would have missed because of big overla…
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Add `dustmasker` as a tool to viral-ngs for pre-processing of metagenomics databases (removal of low-complexity sequences). It's part of the blast toolset so the `Tool` subclass should perhaps be adde…
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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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I have recently used VIBRANT with a metagenomics dataset with very good results, and I wonder if VIBRANT can also be run skipping the recovery step. I have few hundreds viruses that I recovered from s…
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Hello :)
I have a question regarding viral-ngs and its capabilities for detecting virus integration and outputting the results to a text file. I tried to understand the explanation provided in the …
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Many sites that run `toil-cwl-runner`, especially HPC systems, need quite a lot of options defined. It would be nice if there was a config file that formed the basis of the command-line options.
See …
mr-c updated
9 months ago