Add PEAR for merging overlapping paired-end reads

hammerlab / biokepi

Bioinformatics Ketrew Pipelines

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Add PEAR for merging overlapping paired-end reads #378

Open iskandr opened 7 years ago

iskandr commented 7 years ago

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

JPFinnigan commented 7 years ago

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 commented 7 years ago

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.