5. Interpreting the output

MetaCarvel generates a variety of files as output, depending on the options set while running. The files which are useful for downstream analysis are as follows.

1. oriented_links: The list of links between each pair of contigs in an orientation predicted by MetaCarvel algorithm.
2. oriented.gml: The list of links between each pair of contigs represented as a graph in GML format. These can be loaded in MetaGenomeScope for visualization.
3. repeats.txt: The list of repetitive contigs flagged by MetaCarvel's repeat detection algorithm.
4. bubbles.txt: The list of bubbles found by MetaCarvel's variant detection algorithm. Each line in this file contains the start node of the bubble, end node of the bubble followed by the list of nodes in that bubble (including start and end nodes). So, a line like 1 2 1 3 4 2 would mean that this bubble has nodes 1, 2, 3, and 4 and has start node 1 and end node 2.
5. scaffolds.fa: This file contains scaffold sequences generated by MetaCarvel in fasta format.
6. scaffolds.agp: This file contains scaffolds generated by MetaCarvel in AGP format.
7. scaffold_graph.gfa: The scaffold graph in GFA format.
8. mgsc.db: The db file generated by MetagenomeScope if you had set -v true while running MetaCarvel. You can load this file in the MetagenomeScope Web Viewer to visualize the scaffold graph.