Add PEAR for merging overlapping paired-end reads

[iskandr]

http://sco.h-its.org/exelixis/web/software/pear/doc.html

[JPFinnigan]

Apologies if you have already implemented MaSuRCA, but this utility and PEAR seemingly performs a similar function, but MaSuRCA can also be utilized for the "super-read" assembly workflow in StringTie. Link: http://www.genome.umd.edu/masurca.html

Not sure which of two, PEAR or MaSuRCA, will be most useful to you guys going forward.

[iskandr]

It seems like MaSuRCA is much heavier weight since it actually does genome assembly, whereas PEAR will just merge paired reads which seem to overlap due to insufficient fragment/insert size.