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Using the standard 16gb library and some bacterial reads we seem to get empty taxonomic level fields in the kraken2 report file. For example, the root and bacteria lines have no taxonomic level.
br…
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Hi Ming,
I would need a way to indicate clinical isolates and ideally also link to the NCBI BioSample database:
Taxaname_file;NCBI_BioSample
Pseudomonas aeruginosa isolate CH2682;https://www.ncbi…
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Dear all,
Historically, all OXA-258-like beta-lactamases were found in _Achromobacter_ spp., one [paper](https://doi.org/10.1128/jcm.03043-12) considering OXA-258 as a species-specific marker for _…
iorga updated
4 weeks ago
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I run this command with the new version of magnet
`python magnet.py -i ZYMO_D6311_14.nanoq.10.1000.fastq.gz -m ont -o ZYMO_D6311_14.magnet_1 --threads 30 -c relative_abundance.tsv`
i get this error
…
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Hello,
I downloaded and set up the Uniref100 database for the taxonomy pipeline according to the instructions, but when I run the taxonomy command, the output says `Computed index is too large. Avo…
MrOlm updated
4 years ago
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Pseudomonas aeruginosa PA103\u2206UT
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Dear INNUCA team,
Is it possible to run INNUCA for other species than the one listed in the below modules?
https://github.com/B-UMMI/INNUca/tree/master/modules/trueCoverage_rematch
[campylobact…
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Could you provide a minimal example for LCA taxomic classification (diamond db and query sequences) using diamond blastx. I have tested concatenating some genes from different species but it always gi…
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Hello,
Can someone explain this format or have a tool to summarize the outputs?
Something that can take the file and transform by ranking:
121001 root bacteria
100010 root Proteobacteria
I a…
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Hi authors,
I have paired end fastq files of cell free DNA patients infected with sepsis. I have 6 patients files
For these 6 patients the distribution is as follows
Patient 1:
Leuconost…