Toy example of SPARSE

There is a bash script in the examples folder that runs through an example of SPARSE. This example takes reads from an ancient DNA sample of 800 year old Salmonella enterica from this publication.

The contents of the shell script download and create a Bowtie database of some Salmonella genomes (01-03) and then maps some of the ancient reads and displays a report.

sparse init --dbname toyset
sparse index --dbname toyset --seqlist Salmonella_toyset.txt
sparse query --dbname toyset --tag m==a | python ../SPARSE.py mapDB --dbname toyset --mapDB Salmonella --seqlist stdin
sparse predict --dbname toyset --r1 Ragna.sample.fq.gz --workspace Ragna_toy --mapDB Salmonella
sparse report Ragna_toy
cat Ragna_toy/profile.txt
sparse extract --workspace Ragna_toy --ref_id 10