Open jeffreybarrick opened 5 years ago
Here are some example summary files that can be used for testing: https://barricklab.org/release/tmp/ADP1-summary.tgz
HTML table as output.
Could eventually color some cells green/yellow/red to flag suspect files/samples.
In general, the output should have most of the same columns, but additional information, compared to the READ and REFERENCE tables generated for one breseq run. Example:
https://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/REL8593A_output/summary.html
Columns to include in the REFERENCE TABLE:
Columns to include in the READ TABLE
@ginnymortensen
Here is a newer set of breseq output that preserves all of the output folders compared to the one linked above. The output.json
files are still the main place to pull information from.
Motivation: It would be very useful to have a script that can take many runs and create a dashboard for evaluating and comparing their quality/coverage.
It might:
UN
evidence concerning how much of the genome had enough coverage for calling mutations in each sample.Implementation: Most likely as Python/R scripts that generate HTML output. They can parse the
summary.json
files for statistics and usebreseq BAM2COV
to generate files to generate input files for graphing, for example.