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README.rst
check-with-khmer.py
genome-a.fa
genome-b.fa
genome-c.fa
query.in
query.out
reads-a.fa
reads-b.fa
run.sh

README.rst

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