Comments (7)
Okay, so this is what I have for the nanopore data. Anything we want changed?
Runtime
Max. RAM usage
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Looks great. Nothing to change, though I'm wondering what the p values are testing
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I used a wilcoxon signed-rank test. Basically the nonparametric version of a paired t-test (because I'm lazy and couldn't be bothered testing for normality 😅 )
Pretty clear they are not from the plot but I guess it helps if you want to say "significantly different"
It wasn't actually clear to me that the runtimes would be significantly different for drprg and mykrobe
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Here are the Illumina figures. These aren't final as this is only a subset of 400 samples, but I can't imagine it will change dramatically.
Memory
Runtime
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The latest figures after adding in the racon denovo from iqbal-lab-org/pandora#299 can be seen in iqbal-lab-org/pandora#303 (comment)
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Related Issues (20)
- Run TBProfiler HOT 4
- False positive argmatch results HOT 1
- Run drprg HOT 4
- Add grammar for specifying variant "expert" rules
- Parse pandora VCF to detect minor alleles HOT 46
- Update pandora and make_prg HOT 2
- Deal with gene absence HOT 9
- Add some common resistance-conferring mutations that do no exist in population graph HOT 8
- Notice partial gene deletion that spans start codon HOT 8
- Targeted sequencing mode HOT 1
- Disruptive in-frame indels HOT 3
- Lineage calling HOT 1
- Add install instructions to README.md
- How do i pronounce this tool name HOT 1
- Installation_error HOT 2
- Collate_drprg_results HOT 1
- error: unrecognized subcommand 'index' HOT 4
- Paired-end fastq files HOT 1
- Missing expected output file /test/outdir/discover/denovo_sequences.fa HOT 5
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