https://github.com/ctb/2015-sbt-demo
https://github.com/ctb/2015-sbt-demo
Last synced: about 1 year ago
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- Host: GitHub
- URL: https://github.com/ctb/2015-sbt-demo
- Owner: ctb
- Created: 2015-05-30T12:46:11.000Z (about 11 years ago)
- Default Branch: master
- Last Pushed: 2015-06-02T22:26:33.000Z (about 11 years ago)
- Last Synced: 2025-03-26T02:43:07.600Z (over 1 year ago)
- Language: Python
- Size: 121 KB
- Stars: 2
- Watchers: 1
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.rst
Awesome Lists containing this project
README
Demo data for checking out Sequence Bloom Trees,
https://github.com/Kingsford-Group/bloomtree
----
Setup
-----
Build the fake data (genome-a.fa, genome-b.fa, reads-a.fa, reads-b.fa) from
instructions at https://github.com/dib-lab/2015-khmer-wok4-multimap, taking
all output reads (so coverage of ~100).
Make a third fake genome (genome-c.fa) with:
../nullgraph/make-random-genome.py -l 1000 -s 3 --name='genomeC' > genome-c.fa
Execution
---------
Build a bloomtree from reads-a.fa and reads-b.fa with 'run.sh'::
./run.sh
Then, build a query from genomes A and C::
cat genome-a.fa genome-c.fa | grep -v ^'>' > query.in
Run the query::
bt query -t 0.8 c_entire.bf.bv query.in query.out
CTB 5/30/15