Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

full pipeline testing #6

Open
1 of 4 tasks
averagehat opened this issue Feb 25, 2016 · 1 comment
Open
1 of 4 tasks

full pipeline testing #6

averagehat opened this issue Feb 25, 2016 · 1 comment
Assignees
@averagehat
Milestone
Platform Read Sim...

Comments

@averagehat
Copy link
Contributor

Maybe sometime worth doing.

Read simulators:

related project: https://github.com/isovic/overlap-benchmark

these could go in bioconda but they are only a testing dependency and not a part of the framework so the user won't have to install

Data:

  • script to download reference from accession and mutate it etc.
  • blast database
@averagehat averagehat self-assigned this Feb 25, 2016
@necrolyte2 necrolyte2 added this to the Platform Read Simulation milestone Feb 25, 2016
@averagehat
Copy link
Contributor Author

  • generate miseq from reference
  • generate pacbio from reference
  • mutation expected: 1043: A -> G, X%
  • Make/download reference
  • cut ref into X pieces, generate mutations on each piece
  • denovo/mapping

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@averagehat averagehat

Labels
None yet
Projects
None yet
Milestone
Platform Read Simulation
Development

No branches or pull requests
2 participants
@necrolyte2 @averagehat