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Kraken

Kraken is a metagenomic mapping tool that calculates abundances of taxonomic labels in a mixed sample. To use it you can load the existing module kraken/2.1.1 . For a pre-built database refer to the section below.

Demo call:

kraken2 --db /gpfs/project/databases/Kraken2_refseq+hfmv --threads 8 --report kraken.report myReads.fastq

Bracken

Bracken is a complementary tool for species level re-estimation and a compatible module is available: bracken/2.6.0.

Demo call:

est_abundance.py -i kraken.report -k /gpfs/project/databases/Kraken2_refseq+hfmv/kmerDistribution.txt -o bracken.report --out-report bracken.krakenstyle.report

Database

We have a shared database for Kraken2 available at

/gpfs/project/databases/Kraken2_refseq+hfmv

that contains the following organisms:

 - Archaea: 264 genomes (403 contigs), 640.15mb.
 - Bacteria <prokaryotes>: 10753 genomes (20883 contigs), 40490.27mb.
 - Eukaryota: 2192 genomes (7279859 contigs), 78719.21mb.
    davon:
             - Apicomplexa: 2 genomes (21 contigs), 30.84mb.
             - Ascomycota: 1536 genomes (2311006 contigs), 45008.14mb.
             - Basidiomycota: 502 genomes (4496104 contigs), 20111.28mb.
             - Blastocladiomycota: 2 genomes (610 contigs), 93.84mb.
             - Chordata: 2 genomes (6556 contigs), 8498.23mb.
                -> Mensch und Maus
             - Chytridiomycota: 14 genomes (58021 contigs), 742.89mb.
             - Cryptomycota: 2 genomes (1281 contigs), 18.17mb.
             - Microsporidia: 36 genomes (78447 contigs), 239.41mb.
             - Mucoromycota: 74 genomes (193583 contigs), 2985.22mb.
             - Undefined: 6 genomes (2654 contigs), 209.03mb.
             - Zoopagomycota: 16 genomes (131576 contigs), 782.16mb.

 - Viroids: 95 genomes (95 contigs), 0.03mb.
 - Viruses: 27827 genomes (67295 contigs), 939.23mb. 


Update: A newer database has been uploaded (contents: https://genome-idx.s3.amazonaws.com/kraken/pluspfp_20220908/inspect.txt)
and can be found at:

/gpfs/project/databases/Kraken2-2022-09-28

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