Comments (1)
smdabdoub
commented on June 1, 2024
Thanks for bringing KrakenHLL to my attention, I wasn't aware of it previously.
The new format is the same with new columns inserted in the middle. Although your example appears to contain a 'cov' column that is not listed on the KrakenHLL GitHub README.
In any case, as long as you just want the same functionality from kraken-biom with the new format, the changes would be minimal. If you wanted to include the additional columns as metadata in the output BIOM table or use the kmer information to limit which reads are included in the output (for example), that would take some additional work.
from kraken-biom.
Related Issues (20)
- kraken2? HOT 21
- biom file not working with Phinch HOT 3
- Instructions HOT 5
- Updating conda and PyPI HOT 2
- Hi, is there a bracken to biom tool. I have seen this issue requested before but with no conclusion. Thx m
- Errors while using kraken-biom
- Bracken input error: "biom.exception.TableException: Cannot delimit self if I don't have data..." HOT 4
- Abundance calculation question HOT 1
- compatibility with bracken HOT 5
- Add sample_data info to biom file HOT 4
- empty .biom files from normal-looking bracken reports? HOT 4
- New release needed HOT 1
- Include taxonomic levels below species HOT 2
- It seems that unclassified reads are ignored HOT 1
- Question Regarding Read Assignments in Biom Files
- Can you add a new version tag to cite properly?
- Setting --max and --min to the same level causes an error. HOT 1
- Taxonomic hierarchy incorrect for certain cases HOT 8
- it will be great to share the testing examples HOT 1
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