Using pre-built Kraken2 / Bracken DB #26
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Hi all, |
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Replies: 5 comments 6 replies
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Hello and thank you for your interest in Phanta! Question - which taxon are you interested in? We are thinking of expanding the prokaryotic portion of our DB soon to include more species, including those that are lowly prevalent in the human gut. We could definitely help you make the standard K2 database compatible with Phanta if you wish, but please note that it does not include nearly as many viruses as MGV (please see Fig. 3B of our paper). |
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Hi @meenachakra , First, thank you for developing Phanta, which is a very promising workflow. I ran Phanta successfully using the default database (unmasked_db_v1) and integrated_prophages_detector.py which is important to me. I now wish to use Kraken2 database k2_viral_20231009 for Phanta. I have download this database which include Phanta requires like: names.dmp, nodes.dmp, seqid2taxid.map, taxo.k2d, hash.k2d, opts.k2d, inspect.txt (I renamed to inspect.out),and the library/ folder. When I run the pipeline I hit this error: Error in rule filter_kraken: |
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Hi! Thanks for your kind words. This page has a list of the components needed for a Phanta database: https://github.com/bhattlab/phanta/blob/main/databases.md You're probably missing the species_genome_size.txt which can be calculated using the steps here (see Step 3: calculate genome size): Hope this helps! |
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Hi, thank you for your support and fast reply. ok then. One more question. Now I have doubt if k2_viral_20231009 database has the possibility to use for prophages detection using integrated_prophages_detector.py. Which files need to be check, names.dmp, nodes.dmp, or what else? and what I should expect to see on that files which make me sure I can do prophage detection? Thank you in advance. |
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If you "watch" this repo I think you can get updates on when we make changes (and you can manage the notifications in your settings).