smartie-sv

Have contigs and a reference genome? Smartie-sv will align query contigs against a reference genome and call structural variants.

Dependencies

1. Anaconda
2. Snakemake
3. Bedtools

Running

Clone the repo:

git clone --recursive https://github.com/zeeev/smartie-sv.git

Export HDF5LIB if it is NOT in a global path. If the build fails check this first.

Run make:

cd smartie-sv && make

Edit the config in the pipeline folder

Index the reference genome:

bin/sawriter target.fasta

Run the pipeline (Sun Grid Engine):

snakemake -j 10 --cluster-config cluster.config.json --cluster "qsub -l {cluster.h_rt} -l {cluster.mfree} -pe {cluster.pe} -q {cluster.q}" -s Snakefile --verbose -p

Run the pipeline (SLURM):

snakemake -p -w 25 -j 3 --verbose -s Snakefile --cluster-config cluster.config.slurm.json --cluster "sbatch -p {cluster.partition} -n {cluster.n}  -t {cluster.time} -c {cluster.c} -o out -e error" -w 30

Run the pipeline on a local machine:

snakemake -s Snakefile -w 50  -p -k -j 20