ldenti / smg

SMG

Compilation

git clone https://github.com/ldenti/smg.git
cd smg
mkdir build ; cd build
cmake ..
make
cd ..

Prerequisites

• vg
• python3 (+ intervaltree seaborn pandas matplotlib networkx)

Example

cd example
tar xvfz 4.tar.gz
vg construct --progress --threads 4 --reference 4.fa --vcf 4.vcf.gz > 4.pg
vg rna --progress --threads 4 --add-ref-paths --transcripts 4.gtf 4.pg | vg mod --unchop - | vg ids -s - > 4.spliced.pg
vg view 4.spliced.pg > 4.spliced.gfa
python3 ../scripts/reduce_graph.py 4.spliced.gfa > 4.spliced.reduced.gfa
../build/smg gfa 4.spliced.reduced.gfa > minimizers.txt
../build/smg fx 4-reads.fa.gz > minimizers.reads.txt
python3 ../scripts/cluster.py minimizers.txt 4.spliced.pruned.gfa > tree.txt
python3 ../scripts/traverse.py tree.txt minimizers.txt minimizers.reads.txt | sort | uniq -c
# python3 ../scripts/analyze_mmers.py minimizers.txt

TODO