kraken-biom
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smdabdoub
Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).
Hello, I am using kraken-biom script to convert kraken2 report files to a biom file to run in phyloseq R. I managed to produce a unique biom file from 90...
As mentioned above, and thank you very much for this utility.
Dear author, Firstly, I would like to express my appreciation for your excellent work on the kraken-biom software. It has been incredibly useful for my research. However, I have come...
Dear @smdabdoub , Thank you for creating this tool! I noticed that there is an option to export kraken report to a level below species level. Kraken reports the levels...
Thanks a lot for this very handy tool! It makes it very convenient to create a `biom` file and to then use this in `R`, especially in combination with the...
hi Im trying to make .biom files from three sets of reports, 1 from kraken2 and 2 from bracken. The kraken2 and first bracken work fine (theyre both down to...
Hi @smdabdoub, for a bioconda and Galaxy integration we would need a new release tarball. Thanks a lot, Engy and Bjoern
Hello, I have been trying to run kraken on some bracken files I have but there seems to be an issue of compatibility. I have been running the command: kraken-biom...
Hi, I used pip install git+http://github.com/smdabdoub/kraken-biom.git Following which I tried kraken-biom on 2 samples for trial: kraken-biom C1C_S92_krak_out.txt C1T1_S39_krak_out.txt and also kraken-biom C1C_S92_krakenreport.txt C1T1_S39_krakenreport.txt In both cases I ended up...
