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6. Finding Variants
Jay Ghurye edited this page Jan 19, 2019
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To find variants in the scaffold graph generated by MetaCarvel, you can run find_motifs.py
script as follows. Note that you will need to run MetaCarvel pipeline before you run find_motifs.py
.
python find_motifs.py -d metacarvel_output_directory
This would generate several files in the same output directory as follows:
plasmids - the set of cyclic connected components in the graph.
three_bubbles - predicted insertion/deletions. The format is same as bubbles.txt file generated by MetaCarvel.
four_bubbles - predicted simple strain variants with four contigs. The format is same as bubbles.txt file generated by MetaCarvel.
complex_bubbles - predicted complex strain variants with more than four contigs. The format is same as bubbles.txt file generated by MetaCarvel.
tandem_repeats - predicted tandem repeats
repeats - predicted interspersed repeats