ganon

ganon is designed to index large sets of genomic reference sequences and to classify reads against them efficiently. The tool uses Interleaved Bloom Filters as indices based on k-mers/minimizers. It was mainly developed, but not limited, to the metagenomics classification problem: quickly assign sequence fragments to their closest reference among thousands of references. After classification, taxonomic abundance is estimated and reported.

Profile Format

Taxpasta expects a tab-separated file with nine columns. This is generated with the ganon report command. Taxpasta will interpret the columns as:

Column Header	Description
rank
target
lineage
name
nr_unique1
nr_shared
nr_children
nr_cumulative
pc_cumulative

Example

unclassified    -   -   unclassified    0   0   0   174530  27.61288
root    1   1   root    0   0   457530  457530  72.38712
superkingdom    2   1|2 Bacteria    0   0   447016  447016  69.95031
superkingdom    2157    1|2157  Archaea 0   0   10514   10514   2.43680
phylum  1224    1|2|1224    Pseudomonadota  0   0   189513  189513  22.08574

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1. Value used in standardised profile output, representing unambiguous reads that match that reference (i.e., multi-match reads, nor with child reads). See ganon docs for further description. ↩