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I de novo assembly a genome from fastq files and want to remove organelle genomes (mitochondria, chloroplasts, etc.) and plasmids genomes. How should I set up a custom database of organelles and plasm…
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Hi,
GetOrganelle works well for mitochondria and chloroplasts. Do you think it would for assembling bacterial chromosomes or bacterial plasmids?
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kraken-build --standard --db $DBNAME
Only build Bacteria and Viruses, plasmids and human are not downloaded.
Not sure this is a bug or standard feature.
kraken-build --download-library plasmids --db …
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Hello,
https://flanker.readthedocs.io/en/latest/
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I am having difficulty understanding some of the information in the documentation. In order to fully understand and reproduce the information…
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As an enhancement request, it would be nice to have the possibility to choose from more pre-existing configured vectors.
For now only 6 pre-configured vectors are available, it would be nice to ha…
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Because we don't currently have a good way to handling the import of the OpenYeast plasmids, they are appearing in the FASTA for synthesis. As such, any synthesis run needs to exclude them.
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"If you have made functional modifications to the commercial plasmids you obtained, MSKCC would generally consider these new, modified plasmids to be their IP. We always carry out the MTA with the le…
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Derrick,
I notice that often my pure bacterial samples still get 5% say of reads being unclassified. When I assemble these reads, they turn out to be bacterial plasmids.
The problem is that _some_ o…
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### Describe your feature request precisely
QR codes integrated into the main text area of experiments or resources.
The idea is that when one researcher wants to show an experiment to another, b…
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How do I make/use a custom DB?
There are some input files that are not specified
% mob_cluster --mode build -f new_plasmids.fasta -p new_plasmids_mobtyper_report.txt -t new_plasmids_host_taxonom…