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usadellab / Trimmomatic

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Feature Request - report adapter names detected/removed #9

Open chrisgulvik opened 3 years ago

chrisgulvik commented 3 years ago

I use trimmo for adapter clipping and wanted to ask if you'd consider adding a more verbose reporting on what's removed. If it's not done due to the extra compute time, could it be an option to turn on? I don't know of another read filtering package that reports the adapter names removed, but I think it would be valuable to log for routine work as a confirmation the

1. correct adapters were removed and 2. off-target adapters were not removed.

Current Output:

Input Read Pairs: 1773329 Both Surviving: 1284520 (72.44%) Forward Only Surviving: 228498 (12.89%) Reverse Only Surviving: 73383 (4.14%) Dropped: 186928 (10.54%)
TrimmomaticPE: Completed successfully

Example of more verbose output:

Input Read Pairs: 1773329 Both Surviving: 1284520 (72.44%) Forward Only Surviving: 228498 (12.89%) Reverse Only Surviving: 73383 (4.14%) Dropped: 186928 (10.54%)
Adapters Removed: 184542
  TruSeq_Adapter_Index_25: 184532
  I7_Primer_Nextera_XT_Index_Kit_v2_N720: 10
TrimmomaticPE: Completed successfully
TonyBolger commented 3 years ago

Sounds like a useful feature - I think it can be done without adding too much overhead.

bmorledge-hampton19 commented 2 years ago

Was this ever implemented? It would be a very helpful feature to have.