"Clarification on Trimommatic Default Parameters in Kneaddata: Understanding MINLEN Checks for 2x150 bp Data"

Infrastructure and utilities KneadData
1

Dear Biobakery team,

I am trying to understand the default parameters of Trimmomatic when running KneadData with default parameter for 2x150 bp data:

java -jar trimmomatic-0.39.jar PE R_1.fastq R_2.fastq R_1_kneaddata.trimmed.1
.fastq R_1_kneaddata.trimmed.single.1.fastq R_1_kneaddata.trimmed.2.fastq R_1_kneaddata.trimmed.single.2.fastq MINLEN:60 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:8:TRUE SLIDINGWINDOW:4:20 MINLEN:75

Does the first MINLEN:60 check ensure that each processed read should have a minimum length of 60 before trimming? If not, it is discarded. The second MINLEN:75 check then ensures that, after trimming, each read has a minimum length of 75. Is my understanding correct?

Thanks,
Anupam