stampy

[thkuo]

To have Stampy available, some problems need to be dealt with:

• installation
• environment (python2); can be solved by stacking the environments though
• interaction with bwa: It's not recommended to conduct bwa from stampy command but to run bwa before using stampy. Our previous usage, however, directly launches bwa in the command.

[thkuo]

Stampy cannot be installed via conda and requires registration. Can it be directly packaged and redistributed? The README file:

12. License

This is a release version. Permission is granted for the normal use of the program and its output in an academic setting, including in publications. If the program is used to generate data for a publication, please cite this paper:

G. Lunter and M. Goodson. Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res. 2011 21:936-939.

The program itself may not be modified in any way, and may not be reverse-engineered.

This license does not allow the use of this program for any commercial purpose. If you wish to use this program for commercial purposes, please contact the author.

No guarantees are given as to the program's correctness, or the accuracy or completeness of its output. The author accepts no liability for damage or otherwise following from using and interpreting the output of this program. The software is supplied "as is", without obligation by the author to provide any services or support.

[thkuo]

The option of multi-threading (-t) causes the change of mapping result. 1. remove the option as reproducing the old results 2. showing the importance of salmon 3. Where to report it?