interested by the commands used to evaluate accuracy

nanoporetech / ont-assembly-polish

ONT assembly and Illumina polishing pipeline

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interested by the commands used to evaluate accuracy #12

Closed splaisan closed 6 years ago

splaisan commented 6 years ago

HI, I liked a lot your evaluation but do not find which lastal and mummer commands you used to get to the shown histograms. If you have time, could you please share a bit more on the analysis you did, I would like to repeat it with my own yeast data from Sequel and minION to compare the outcomes. Thanks

bsipos commented 6 years ago

Hi,

The accuracies were calculated using the compare_genomes_lastal.py and compare_genomes_dnadiff.py scripts from the wub package. They call lastal (with parameters -a 1 -b 1) and dnadiff (with default parameters) respectively. The scripts then parse the results and in the case of lastal filter for the best scoring alignments. Let me know if you have any more questions.

Cheers, Botond