Do I need to use dedup.sh or clumpify.sh to do dereplicate with BBmap?
BBMap short read aligner, and other bioinformatic tools.
Brought to you by:
brian-jgi
Menu
▾
▴
Dear developer
As we noticed that their are two scripts can be used to do deduplicate of reads for shotgun metagneome data (prepared by Illumina Nextera pre, which usually have PCR artifacts). The dedup.sh and clumpify.sh both can do this work.
We tried both methods and find that they are not consistant with each other. The dedup.sh remove more reads than the clumpify.sh, we raise a question of which script should be used for this task.
Looking forward to your reply
Regards.
Xiaotao