bqtools has some nice features that make it easy to work with existing sequencing data. One of these is recursive encoding - which will convert all the sample pairs in a directory (and subdirectories) to their BINSEQ representation.

Let’s try it out with all the sample pairs we have in the data directory:

Oh, there is a warning!

Let’s take a look at the files that were created:

We can see that we have 8 VBQ files with an R1 or R2 - but we’ve learned we do not need to keep these files separate.

The --recursive flag tells bqtools to convert every individual file to a BINSEQ file. But it also correctly identified that the files in this directory appear to be paired. So it converted each individual file and did not pair them - but it warned us that this might not be what we wanted.

Let’s remove those individual files that were not correctly paired and try again:

Now let’s try again with the --paired flag:

Great! Now we have exactly what we want - 4 files that are paired: