6. Finding Variants

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