Equivalent commands on different trimming tools for comparison

Question

[pubsurfted]

Hello everyone,

I would like to compare the following trimming tools' outputs: Trimmomatic, TrimGalore, FastP. For consistency, I want to trim fastq files with these trimming tools with same parameters/flags. What would be the basic equivalent commands of these trimming tools for paired-end reads of length=100 obtained by illumina 1.9?

[pubsurfted]

For trimmomatic I have used this:

java -jar trimmomatic-0.39/trimmomatic-0.39.jar PE -threads 4 \
fastq/stem_1.fastq.gz fastq/stem_2.fastq.gz \
~/data/trimmomatic/stem_1.trimmed.fastq ~/Desktop/stem_1un.trimmed.fastq \
~/data/trimmomatic/stem_2.trimmed.fastq ~/Desktop/stem_2un.trimmed.fastq \
ILLUMINACLIP:trimmomatic-0.39/adapters/TruSeq3-PE-2.fa:2:30:10

For trimgalore! I have used this:

trim_galore --paired --illumina --fastqc ~/fastq/flower_1.fastq ~/fastq/flower_2.fastq -o ~/data/trimgalore

For Fastp I'm not sure. As for the above code, I'm unsure if they have equivalent flags.

[Mensur Dlakic]

Why isn't this a direct answer rather than comment?

[pubsurfted]

I am not sure if it is correct. I'm looking for help.

Answer 1

[Istvan Albert]

there are subtle differences in how tools work, and I found it surprisingly difficult to produce the exact same QC output with different tools, some behaviors are not well explained

for example, the trimmomatic window trim operates from left to right, whereas most other tools trim from the right to the left. The trimmomatic parameters of:

SLIDINGWINDOW:4:30   MINLEN:150

will be equivalent to the fastp flags of:

--cut_window_size 4 --cut_mean_quality 30 --cut_right -l 150

trimmomatic does not support left to right window trim, whereas fastp does.

[pubsurfted]

Thank you so much! That's very helpful.