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sn_kraken.pl.md

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SYNOPSIS

sn_kraken.pl

Runs Kraken1 on a sample.

Software requirements

  • Kraken1
  • Database formatted for Kraken1

Algorithm

Runs Kraken1 on a sample. It looks for raw sequence reads (fastq) as input. If not found, runs on genome assemblies under runDir/SneakerNet/assemblies/sampleName/something.fasta.

Outputs

No table output. Creates files under runDir/SneakerNet/kraken/sampleName:

  • kraken.report - a summary of counts per taxon with the following fields. More information here: https://ccb.jhu.edu/software/kraken/MANUAL.html#sample-reports
    • Percentage of reads covered by the clade rooted at this taxon
    • Number of reads covered by the clade rooted at this taxon
    • Number of reads assigned directly to this taxon
    • A rank code, indicating (U)nclassified, (D)omain, (K)ingdom, (P)hylum, (C)lass, (O)rder, (F)amily, (G)enus, or (S)pecies. All other ranks are simply '-'.
    • NCBI taxonomy ID
    • indented scientific name
  • kraken.filtered.report - the same as above, but all hits < 1% are removed
  • kraken.taxonomy - a tab-delimited file
    • first column is the number of reads
    • second column, and all subsequent columns are the taxonomy starting with root and going down as far as possible, e.g., scientific name.
  • report.html - graphical output in Krona format