SEQanswers - View Single Post - Introducing BBDuk: Adapter/Quality Trimming and Filtering

Brian Bushnell · 04-18-2017, 10:08 AM

The difference is primarily because you are quality-trimming to Q27, which is too high for almost any purpose. I'd suggest a command more like this:

Code:

bbduk.sh -Xmx8g in=D3_464_S2_L001_R1_001.fastq.gz out=D3_464_S2_L001_R1_001_trimmed.fastq.gz ref=resources/adapters.fa threads=8 k=19 mink=5 hdist=1 hdist2=0 ktrim=r qtrim=r minlength=36 trimq=14

04-18-2017, 10:08 AM	#215
Brian Bushnell Super Moderator Location: Walnut Creek, CA Join Date: Jan 2014 Posts: 2,707	The difference is primarily because you are quality-trimming to Q27, which is too high for almost any purpose. I'd suggest a command more like this: Code: bbduk.sh -Xmx8g in=D3_464_S2_L001_R1_001.fastq.gz out=D3_464_S2_L001_R1_001_trimmed.fastq.gz ref=resources/adapters.fa threads=8 k=19 mink=5 hdist=1 hdist2=0 ktrim=r qtrim=r minlength=36 trimq=14