metaplasmidspades --assembly-graph

[INFINITY1993]

Hi,
I want to recover plasmids by directly using .gfa file that generated during the metaspades assembly, whereas there are three .gfa files (assembly_graph_after_simplification.gfa, assembly_graph_with_scaffolds.gfa, and strain_graph.gfa). Which one should I use?
Thanks!

[asl]

The answer is available from the spades.log file, e.g.:

 * Assembled contigs are in <path>/contigs.fasta
 * Assembled scaffolds are in <path>/scaffolds.fasta
 * Paths in the assembly graph corresponding to the contigs are in <path>/contigs.paths
 * Paths in the assembly graph corresponding to the scaffolds are in <path>/scaffolds.paths
 * Assembly graph is in <path>/assembly_graph.fastg
 * Assembly graph in GFA format is in <path>/assembly_graph_with_scaffolds.gfa

Same information could be found in the manual: https://cab.spbu.ru/files/release3.15.5/manual.html#spadesoutput

Hope this helps

[asl]

Consider using the latest SPAdes.

[INFINITY1993]

OK, Thanks!

[INFINITY1993]

Hi, dear asl,
In the latest version of spades, I did successfully run the metaplasmidspades. But it seems that it would succeed regardless of whether the --assembly-graph was configured or not. Thus, it confused me whether and how the metaplasmidspades takes the spades-generated assembly graph as input.

[asl]

Well, the duration should be different. As well as the output :)

[INFINITY1993]

OK, Thanks!