How to get summary statistics out of bbduk.sh ?

How to get summary statistics out of bbduk.sh ?

1

I am using bbduk to quality trim my raw sequencing reads but would like to get more summary statistics out of it than the default. I can see many options for pre-made histograms of the statistics I would like but not to get the raw numbers as I would rather the generate the plots myself! Is there a way to do this that I am missing?


quallity


sequencing


control

• 44 views

Capture the stderr stream from your bbduk jobs. You should get the following

Input:                          12202091 reads          610104550 bases.
KTrimmed:                       9227056 reads (75.62%)  254394193 bases (41.70%)
Total Removed:                  1328490 reads (10.89%)  254394193 bases (41.70%)
Result:                         10873601 reads (89.11%)         355710357 bases (58.30%)


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