Determining number of merge-able reads

[cheezemeister]

At the moment I'm working mostly with 2 x 300 bp PE data from the V3V4 region of 16S. Can someone suggest a method for me to determine how many of the read pairs in my data are mergeable, preferably with me being able to specify the amount of overlap (e.g. minimum 20 base pairs)?

Thanks!

[Brian Bushnell]

I suggest running BBMerge. It has a "minoverlap" flag (default 12). In this case, for input read1.fq and read2.fq:

bbmerge.sh in=read#.fq out=merged.fq outu=unmerged.fq minoverlap=20

If all you want is to know the percent that is mergeable, then remove the "out" and "outu" flags and add the flag "reads=1m", so it will stop after a million reads and just print the merge rate.