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kraken2
Young edited this page Feb 9, 2024
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kraken2 is a useful tool for identification of possible inter-species contamination. The kraken2 subworkflow is an optional workflow that requires a kraken2 database. Instructions on how to download a Kraken2 database can be found on a different wiki page.
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kraken2
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flowchart LR
fastq --> kraken2
database --> kraken2
params.kraken2_db = ""
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- amrfinderplus
- bbduk
- blastn
- blobtools_*
- core_genome_evaluation
- circulocov
- datasets_*
- drprg
- elgato
- emmtyper
- fastani
- fastp
- fastqc
- heatcluster
- iqtree2
- kaptive
- kleborate
- kraken2
- mash_*
- mashtree
- mlst
- multiqc
- mykrobe
- panaroo
- pbptyper
- phytreeviz
- plasmidfinder
- prokka
- quast
- seqsero2
- serotypefinder
- shigatyper
- snp_dists
- spades