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I am not 100% sure whether this is a bug or just an unexpected behaviour ...
I am using Mykrobe 0.8.1 with Mac OS X Catalina.
I have a folder containing three BAM files:
```
Taras-iMac:BAM a…
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Hi,
I am getting ≃ 2.5 more duplicates marked in `snap paired with -so parameter` than with `snap paired without -so option + pipe to samtools markdup or picard MarkDuplicates`.
Stats obtained with …
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@mbhall88 has been running "latest" Pandora with the perf changes you 3 produced on the full graph with a cardio sample. So far running for days, sitting in the "get intervals" stage.
@mbhall88 feel …
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To infer organisms form the fastQ samples, the top most over-represented organisms in [SRA](https://www.ncbi.nlm.nih.gov/sra) are being selected based on the following parameters:
- Fraction of sam…
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Session info
```r
─────────
setting value
version R version 3.6.3 (2020-02-29)
os Ubuntu 18.04.5 LTS
system x86_64, linux-gnu
ui …
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Hi,
I am getting low % of properly paired reads in _snap paired_ comparatively to _bwa mem_ (24.19% vs 99.34%). These are values for trimmed input. Without trimming, I get 0% properly paired reads …
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See https://github.com/DerrickWood/kraken/issues/127 for original submission. Example output line (with initial "C" but taxid 0) is below:
`C M00963:162:000000000-AHPVV:1:1101:14752:1397 0 123|123 …
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I have run the following command and got an issue. How can I solve it?
$ '/home/genomic-lab/anaconda3/envs/pyppi/bin/run_gubbins.py' -p gubbins clean.full.aln
--- Gubbins 2.4.1 ---
Crouch…
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![image](https://user-images.githubusercontent.com/453972/70183066-3059fd00-1739-11ea-97dd-0d7db5d02519.png)
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Hello,
I am trying to get susceptibility for a M. tuberculosis genome, the output is giving me this:
tb_sample_id": {
"susceptibility": {},
"phylogenetics": {
"phylo…