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graph_run.sh
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echo "Mapping reads with minigraph..."
./minigraph/minigraph -t32 -cx lr CHM13Y_95H.gfa Reads/CHM13_reads_5%.fa > Results/minigraph/CHM13Y_95H_5%.gaf
./minigraph/minigraph -t32 -cx lr CHM13Y_80H.gfa Reads/CHM13_reads_5%.fa > Results/minigraph/CHM13Y_80H_5%.gaf
./minigraph/minigraph -t32 -cx lr CHM13Y_40H.gfa Reads/CHM13_reads_5%.fa > Results/minigraph/CHM13Y_40H_5%.gaf
./minigraph/minigraph -t32 -cx lr CHM13Y_10H.gfa Reads/CHM13_reads_5%.fa > Results/minigraph/CHM13Y_10H_5%.gaf
echo "Mapping reads with minichain..."
../minichain -t32 -cx lr CHM13Y_95H.gfa Reads/CHM13_reads_5%.fa > Results/minichain/CHM13Y_95H_5%.gaf
../minichain -t32 -cx lr CHM13Y_80H.gfa Reads/CHM13_reads_5%.fa > Results/minichain/CHM13Y_80H_5%.gaf
../minichain -t32 -cx lr CHM13Y_40H.gfa Reads/CHM13_reads_5%.fa > Results/minichain/CHM13Y_40H_5%.gaf
../minichain -t32 -cx lr CHM13Y_10H.gfa Reads/CHM13_reads_5%.fa> Results/minichain/CHM13Y_10H_5%.gaf
echo "Mapping reads with GraphAligner..."
/usr/bin/time -v ./bin/GraphAligner -t32 -x vg -g CHM13Y_95H.gfa -f Reads/CHM13_reads_5%.fa -a Results/GraphAligner/CHM13Y_95H_5%.gaf
/usr/bin/time -v ./bin/GraphAligner -t32 -x vg -g CHM13Y_80H.gfa -f Reads/CHM13_reads_5%.fa -a Results/GraphAligner/CHM13Y_80H_5%.gaf
/usr/bin/time -v ./bin/GraphAligner -t32 -x vg -g CHM13Y_40H.gfa -f Reads/CHM13_reads_5%.fa -a Results/GraphAligner/CHM13Y_40H_5%.gaf
/usr/bin/time -v ./bin/GraphAligner -t32 -x vg -g CHM13Y_10H.gfa -f Reads/CHM13_reads_5%.fa -a Results/GraphAligner/CHM13Y_10H_5%.gaf
./k8 mgutils.js stableGaf CHM13Y_10H.gfa Results/GraphAligner/CHM13Y_10H_5%.gaf > Results/GraphAligner/CHM13Y_10H_5%_stable.gaf
./k8 mgutils.js stableGaf CHM13Y_40H.gfa Results/GraphAligner/CHM13Y_40H_5%.gaf > Results/GraphAligner/CHM13Y_40H_5%_stable.gaf
./k8 mgutils.js stableGaf CHM13Y_80H.gfa Results/GraphAligner/CHM13Y_80H_5%.gaf > Results/GraphAligner/CHM13Y_80H_5%_stable.gaf
./k8 mgutils.js stableGaf CHM13Y_95H.gfa Results/GraphAligner/CHM13Y_95H_5%.gaf > Results/GraphAligner/CHM13Y_95H_5%_stable.gaf
echo "Mapping reads with GraphChainer..."
/usr/bin/time -v ./bin/GraphChainer -t32 -g CHM13Y_95H.gfa -f Reads/CHM13_reads_5%.fa -a Results/GraphChainer/CHM13Y_95H_5%.gaf
/usr/bin/time -v ./bin/GraphChainer -t32 -g CHM13Y_80H.gfa -f Reads/CHM13_reads_5%.fa -a Results/GraphChainer/CHM13Y_80H_5%.gaf
/usr/bin/time -v ./bin/GraphChainer -t32 -g CHM13Y_40H.gfa -f Reads/CHM13_reads_5%.fa -a Results/GraphChainer/CHM13Y_40H_5%.gaf
/usr/bin/time -v ./bin/GraphChainer -t32 -g CHM13Y_10H.gfa -f Reads/CHM13_reads_5%.fa -a Results/GraphChainer/CHM13Y_10H_5%.gaf
./k8 mgutils.js stableGaf CHM13Y_10H.gfa Results/GraphChainer/CHM13Y_10H_5%.gaf > Results/GraphChainer/CHM13Y_10H_5%_stable.gaf
./k8 mgutils.js stableGaf CHM13Y_40H.gfa Results/GraphChainer/CHM13Y_10H_5%.gaf > Results/GraphChainer/CHM13Y_40H_5%_stable.gaf
./k8 mgutils.js stableGaf CHM13Y_80H.gfa Results/GraphChainer/CHM13Y_10H_5%.gaf > Results/GraphChainer/CHM13Y_80H_5%_stable.gaf
./k8 mgutils.js stableGaf CHM13Y_95H.gfa Results/GraphChainer/CHM13Y_95H_5%.gaf > Results/GraphChainer/CHM13Y_95H_5%_stable.gaf
echo "Mapped reads to graphs"