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@@ -71,7 +71,7 @@ The following inputs are required to run the `metacoag` subcommand.
* Contigs file
* Assembly graph file(s)
* A delimited file containing the contig identifier and its average read coverage for each contig - can be obtained by running a read coverage calculation tool such as CoverM [Woodcroft:2017] or Koverage [@Roach:2024]
* A delimited file containing the contig identifier and its average read coverage for each contig - can be obtained by running a read coverage calculation tool such as CoverM [@Woodcroft:2017] or Koverage [@Roach:2024]
The assembly graph files can vary depending on the assembler used to generate the contigs. The metaSPAdes version requires the assembly graph file in `.gfa` format and the paths file corresponding to the contigs file in `.paths` format. The MEGAHIT version requires the assembly graph file in `.gfa` format. The metaFlye version requires the assembly graph file `assembly_graph.gfa` and the paths file `assembly_info.txt` from the final assembly output.
