sbx_krakenuniq

Installation KrakenUniq🐙

Make sure you have the latest version of KrakenHLL installed.

git clone https://github.com/fbreitwieser/krakenuniq.git
cd krakenuniq
bash install_krakenuniq.sh $HOME/bin/
export PATH=$PATH:$HOME/bin/

Build KrakenHLL database for Bacteria complete genomes

DBNAME=bacteria
krakenuniq-download --db $DBNAME taxonomy
krakenuniq-download refseq/bacteria --db $DBNAME --dust --threads 20

krakenuniq-build -build --db $DBNAME --jellyfish-hash-size 6400M \
              --taxids-for-sequences --taxids-for-genomes --threads 8
dump_taxdb taxDB taxonomy/names.dmp taxonomy/nodes.dmp

Build KrakenHLL database for Virus all genomes

DBNAME=virus-neighbors
krakenuniq-download --db $DBNAME taxonomy
krakenuniq-download refseq/viral/Any --db $DBNAME --dust --threads 8
krakenuniq-download viral-neighbors --db $DBNAME --dust --threads 8

krakenuniq-build -build --db $DBNAME --kmer-len 25 \
              --jellyfish-hash-size 6400M \
              --taxids-for-sequences --taxids-for-genomes --threads 8
dump_taxdb taxDB taxonomy/names.dmp taxonomy/nodes.dmp

Usage

With you sunbeam conda environemnt activated,

1. Clone into your Sunbeam directory:

git clone https://github.com/zhaoc1/sbx_krakenhll

2. Add the new config options to your config file

cat sunbeam/extensions/sbx_krakenhll/config.yml >> sunbeam_config.yml

3. Run time

snakemake --configfile my_config.yml all_krakenhll

4. Fun part

Try to play with krakenhll-extract-reads to get the classified reads for your favoriate taxid 😬