Kozich et al. 2013 VS Fadrosh et al. 2014

Journal club
1

Hey,

I am quite curious to know your thoughts on the Fadrosh paper. I know that Illumina also have a standard method of doing V3-4, although many sources suggest it would be better to stick with V4 or any other where you would have complete overlap of paired ends. What are your thoughts? Very tempted to sequence a larger fragment as many do and ignore the error scores? Or do the right thing, sacrifice resolution and do it right.

Kozich et al

Fadrosh et al

2

Where to begin. Their method is not “improved”. They do not present error rates. They use N’s to stitch together reads that do not overlap. Need I go on?