When quality trimming raw reads to a phred score with many of the numerous tools out there (I prefer to use bbduk), there is often conflicting advice surrounding to what Q score one should filter too.
I have read many of Brian Bushnell's (the mind behind bbtools) post and replies and from what I gather there really is no right answer as it depends on what you want to do.
Say for example I have some illumina short reads and some pacbio long reads that I will to do the following with:
- Hybrid assembly
- Illumina only de novo assembly
- Pacbio only de novo assembly
I have been previously told that a score of Q30 is highly typical to use however I have read that anything above 27 is just unnecessary and potentially damaging to generating good assemblies. On the bbduk help pages on Seqanswers Q10 is used in every example.
Thus is Q10 a good general base point for quality trimming to provide decent assemblies or is this also to high?
How one one work out the above on their own without needing to come here to answers?
Secondly, should we trim pacbio reads in either a hybrid assembly or pacbio de novo assembly?