Version 3.0 offers an opportunity to change some default settings. Let's list them here.
make-consensi.py
--aligner: biopython
Currently it's swalign, an esoteric Smith Waterman implementation.
That'll require BioPython as a dependency, though.
- Ideally version 1.75 at least
--cons-thres: 0.7
Currently set to 0.5, but it should default to the threshold recommended by the duplex sequencing designers in Kennedy et al. 2014 (page 4).
correct.py
--dist: 3
Currently it's 1, but a more aggressive setting is still pretty safe. I've already changed the default in the Galaxy tool.
Version 3.0 offers an opportunity to change some default settings. Let's list them here.
make-consensi.py
--aligner
:biopython
Currently it'sswalign
, an esoteric Smith Waterman implementation. That'll require BioPython as a dependency, though. - Ideally version 1.75 at least--cons-thres
:0.7
Currently set to0.5
, but it should default to the threshold recommended by the duplex sequencing designers in Kennedy et al. 2014 (page 4).correct.py
--dist
:3
Currently it's1
, but a more aggressive setting is still pretty safe. I've already changed the default in the Galaxy tool.