I am trying to improve our DNA sequencing work-flow. I choose a software called AdapterRemoval for quality trimming and merging overlapping reads. I try to benchmark AdapterRemoval against the previous software called sickle with the same parameter and I don't understand why I have so many difference.
this is the sickle command with the minimum quality of 20 and minimum read length of 30 :
sickle pe -t illumina -f multiplex_bad_contam_1.fq -r multiplex_bad_contam_2.fq -q 20 -l 30 -o trimmed_multiplex_bad_contam_1_si.fq -p trimmed_multiplex_bad_contam_2_si.fq -s removed_sample_si.fq
This is the AdapterRemoval command the minimum quality and minimum length are the same:
AdapterRemoval --file1 multiplex_bad_contam_1.fq --file2 multiplex_bad_contam_2.fq --qualitybase 64 --trimqualities --minquality 20 --minlength 30 --output1 trimmed_multiplex_bad_contam_1_ar.fq --output2 trimmed_multiplex_bad_contam_2_ar.fq --singleton removed_sample_ar.fq
if someone have an idea it would be great.
thank for your help,
ps: I apologise for the English mistakes but I am not naturally English speaker.