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Primer filtering with bbduk / bbduk2.sh

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  • Primer filtering with bbduk / bbduk2.sh

    Hello,

    I have merged Illumina reads and try to filter out all reads that have both, a recognisable fwrd and a recognisable reverse primer and then to trimm those primers.

    And I'd like to do this in as few commands as possible.

    So far I am using the following code for filtering. Note that if I specify a restrictleft & restrictleft argument no primers are found for some reason

    Code:
    bbduk2.sh in=16S_analysis/XXX.fna \
                            fliteral=CCTACGGGNBGCASCAG,GACTACNVGGGTATCTAATCC \
                            minkmerhits=2 \
    			k=17 \
    			copyundefined \
    			rcomp=t \
    			hammingdistance=1 \
    			outm='16S_analysis/with_Primer.fasta' \
    			out='16S_analysis/no_F_Primer.fasta' \
    			stats='16S_analysis/Primer_stats.txt'\
                            overwrite=true \
    			-Xmx6g
    I can now take this file a search for the foward primer, trimm with lliteral and then do it for the reverse primer. But this is not ideal. Can it be done in one step?

    thanks!

    Fabian
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