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pirovc / ganon

ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more
https://pirovc.github.io/ganon/
MIT License
86 stars 13 forks source link

Feature/optimize default params #225

Closed pirovc closed 1 year ago

pirovc commented 1 year ago

--window-size 31 --kmer-size 19 --rel-cutoff 0.75 (python) --rel-filter 0.0 --report-type abundance

codecov-commenter commented 1 year ago

Codecov Report

Merging #225 (25b0a1d) into dev (5ac7e5f) will increase coverage by 0.09%. The diff coverage is 100.00%.

@@            Coverage Diff             @@
##              dev     #225      +/-   ##
==========================================
+ Coverage   86.59%   86.69%   +0.09%     
==========================================
  Files          22       22              
  Lines        2977     2999      +22     
==========================================
+ Hits         2578     2600      +22     
  Misses        399      399
Impacted Files Coverage Δ
src/ganon/classify.py 89.47% <ø> (ø)
src/ganon/config.py 81.54% <100.00%> (ø)
src/ganon/report.py 92.30% <100.00%> (+0.47%) :arrow_up:

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