Closed kapsakcj closed 3 years ago
Curtis,
Since V1.0.0, we recommend allele micro assembly as the default workflow. According to our evaluation, it is more accurate than K-mer based workflows and provides additional benefit of potential inter-serotype contamination detection. K-mer is faster and best suited for high throughout applications.
Best, Xiangyu
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On May 7, 2019, at 2:22 PM, Curtis Kapsak notifications@github.com<mailto:notifications@github.com> wrote:
In the USAGE section of the readme, it states that the default mode is allele mode:
Usage: SeqSero2_package.py
-m
Although in the SeqSero2 v1.0.0 release, it shows that the k-mer mode is default (and I believe runs k-mer mode as default, too):
usage: SeqSero2_package.py -t
Developper: Shaokang Zhang (zskzsk@uga.edumailto:zskzsk@uga.edu), Hendrik C Den-Bakker (Hendrik.DenBakker@uga.edumailto:Hendrik.DenBakker@uga.edu) and Xiangyu Deng (xdeng@uga.edumailto:xdeng@uga.edu)
Contact email:seqsero@gmail.commailto:seqsero@gmail.com
optional arguments:
-h, --help show this help message and exit
-i I [I ...]
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OK, thanks for clarifying, Xiangyu. It might be a good idea to edit the help options that appear when you run SeqSero2_package.py
to reflect your recommendation.
Best, Curtis
In the USAGE section of the readme, it states that the default mode is allele mode:
Although in the SeqSero2 v1.0.0 release, it shows that the k-mer mode is default (and I believe runs k-mer mode as default, too):