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allenday/Merge Cannabis Draft Genome Assemblies.bash

Last active February 1, 2017 23:36
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Merge Cannabis Draft Genome Assemblies.bash
git clone https://github.com/cbib/MIX.git
./MIX/bin/preprocessing.py -o contigs.fa AGQN01.1.fsa_nt AGQN01.2.fsa_nt LKUA01.1.fsa_nt LKUA01.2.fsa_nt LKUB01.1.fsa_nt MNPR01.1.fsa_nt MNPR01.2.fsa_nt
nucmer --maxmatch --prefix alignments contigs.fa contigs.fa
show-coords -rcl alignments.delta > alignments.coords
./MIX/bin/Mix.py -a alignments.coords -c contigs.fa -o output_dir/ -C 300 -A 200
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