VSEARCH 2.17.0
The fastq_mergepairs command has been changed. It now allows merging of sequences with overlaps as short as 5 bp if the --fastq_minovlen option has been adjusted down from the default 10. In addition, much fewer pairs of reads should now be rejected with the reason 'multiple potential alignments' as the algorithm for detecting those have been changed. The orient command has also been improved.