What quality trimming options can be used with prinseq? I intend to use a min qual of 20 and would like to trim from the right and retian those reads that have a min length of 30. What window size is good? I want to de novo assemble a genome with these reads.
You can check the manual/in-line help for prinseq program to get this type of information.
I would recommend that you use bbduk.sh from BBMap suite. You can easily understand options you need. e.g. in your case trimq=20 minlen=30.
fastp is a good tool for your task. Run fastp with:
fastp -i in.fq -o out.fq -3 -W 6 -M 20 -l 30
-i in.fq specifies the input fastq file
-o out.fq specifies the output fastq file after filtering
-3 enables the sliding window cutting in 3'
-W 6 specifies 6 as the sliding window size for quality cutting
-M 20 specifies Q20 as the mean quality requirement within the sliding window
-l 30 indicates that reads shorter than 30bp will be discarded
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version 2.3.6
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My reads are 150 bases long. Chan, do you suggest 6 as the sliding window? How does one decide?
I think 4~6 window size is good to try with.
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ADD COMMENT/ADD REPLYwhen responding to existing posts to keep threads logically organized.This should have gone under @Chen's answer below.