kraken2 db

[kopardev]

Change kraken2 db on biowulf to include Mouse

[kopardev]

database created using

#!/usr/bin/env bash

module load kraken
module load fastx_toolkit

DBNAME="CCBR_custom_db"

kraken2-build --download-taxonomy --db $DBNAME --threads 8
kraken2-build --download-library bacteria --db $DBNAME
kraken2-build --download-library viral --db $DBNAME
kraken2-build --download-library UniVec_Core --db $DBNAME
kraken2-build --download-library human --db $DBNAME

ln -s /data/CCBR_Pipeliner/db/PipeDB/Indices/mm10_basic/mm10.fa
fasta_formatter -i mm10.fa -w0 -o mm10.w0.fa
cat mm10.w0.fa |awk '{if ($1~/^>/) {print $1"|kraken:taxid|10090"} else {print}}' > mm10.w1.fa
split -l 2 mm10.w1.fa
find . -maxdepth 1 -name 'xa?' -print0 | xargs -0 -i{} -n1 kraken2-build --add-to-library {} --db $DBNAME

kraken2-build --build --threads 32  --db $DBNAME 
kraken2-buid --clean --db $DBNAME

[kopardev]

Copied in /data/CCBR_Pipeliner/db/PipeDB/kraken2/CCBR_custom_db Also saved at s3://nciccbr/Resources/common/CCBR_custom_db

[kopardev]

To do:

• [x] test the krakendb
• [x] change location on biowulf config file and next RENEE release
• [x] repeat for FRCE as well

[kopardev]

Done in v2.4