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when build databases jellyfish error on the first step and no other details .
Found jellyfish v1.1.12
Kraken build set to minimize disk writes.
Found 12 sequence files (*.{fna,fa,ffn,fasta,fsa}) …
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If it's possible to have lineage tax id instead of full name ?
```
taxid kindom phylum class order family genus species
11138 10239 2732408 2732506 76804 11118 694002 694005
123595 10239 273240…
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Hello, it's me again.
I wondered if the Microeukaryotic DB can be used with the MMSEQS2 taxonomy module. I am interested in using this database to assign taxonomy at the contig level rather than t…
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Hi,
Thanks for creating this tool.
I have downloaded the nr protein database using the following commands,
kraken2-build --download-taxonomy --DB nr
kraken2-build --download-library nr --DB nr
k…
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https://github.com/DerrickWood/kraken2/blob/acc22481bbeb32b870c12b403ce595fe7a6db770/src/mmscanner.cc#L181C35-L181C35
When the first k characters of seq are all fuzzy characters, if "str_pos_ >= (s…
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Dear pioneers for much improved pathogen detection,
we have an example from nanopore (resulting in long reads > 1500 bps) where the kraken1-part of krakenuniq counts over 12000 kmers (k = 31) for a…
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This is a requested feature for the taxon assignment phase of the autometa pipeline (Thanks @tderond for bringing this to my attention).
This would involve outputting an additional column or colum…
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## Expected Behavior
Run mmseqs databases to create a taxonomic database that uses recent data from uniref, e.g uniref100
## Current Behavior
A recent downloaded uniref100 fasta file has 342650…
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Hi again! My supervisor and I have been troubleshooting our efforts to update the GTDB_release207 pre-made custom database with a selection of genomes from JGI GOLD (see previous issue #29). Based on …
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Hi,
the Debian packaged kraken has added a simple test suite that used to work with version 0.10.5 but stoped working since version 1.0. Some investigation has shown that the fasta examles (for inst…