Shorter read length

[robbueck]

Hi,
I'm working on a dataset where the reads are around 60 bp long after trimming. would it be possible to have a database that allows read_length to be 60 bp?
Thank you in advance
Rob

[meenachakra]

Hello, yes! You can create this yourself by activating your Phanta environment and executing the bracken-build command here, with read length 60 (default value for k) -
https://github.com/jenniferlu717/Bracken#step-1-generate-the-bracken-database-file-databasexmerskmer_distrib

let us know if you have any questions!

[robbueck]

I've tried that, but I'm not sure what I should give as database location. If I give the folder with the phanta database (unmasked_db_v1) it creates empty files. From what I get from the bracken docs, it seems that it misses a fasta file in the library dir?

[meenachakra]

Ah, I see, thanks for letting us know!
You can find the fna files here:
wget http://ab_phanta.os.scg.stanford.edu/Phanta_DBs/database_V1.library.tar.gz

You can download that into the database folder, untar it and rename it library if necessary... let us know if that works!

[zhixuanyan]

Hello, I have downloaded the updated database (HumGut + UHGV "HQ+"), but the read length of the bracken database in this database is 150bp. I want to build a bracken database with a read length of 100 bp, but I don't have the genome file for ' HumGut + UHGV "HQ+" ' databse , can you tell me where to download it? Very much looking forward to your reply, thank you.

[meenachakra]

Sure! Will update soon.

[meenachakra]

Here you go! You can download this directly. Let us know if it doesn't work for you.
100mers_humgut_uhgv_hqplus.zip

[meenachakra]

We're currently having some technical difficulties uploading to the repository that we normally upload to, but hopefully this will be resolved shortly. If not, we will share the 75bp Bracken DB with you.

[zhixuanyan]

OK, thanks.

[meenachakra]

We're unfortunately not able to figure it out - but here is the 75bp file in the meantime!
75mers_kmer_distrib.zip

[zhixuanyan]

Thank you so much.

[meenachakra]

We've resolved the issue with the object store - and you can now download all the sequences using:

wget http://ab_phanta.os.scg.stanford.edu/Phanta_DBs/humgut_uhgv_hqplus_library.tar.gz