Right GFA file to use?

[GeoMicroSoares]

Hi there - I've assembled a metagenome with metaSPAdes and now want to use the resulting GFA with phables - my question is, what GFA is the correct GFA? Here's what I have from the assembly directory:

ll mgshot_S7938Nr1_metaspades3.15.5/*.gfa
mgshot_S7938Nr1_metaspades3.15.5/assembly_graph_after_simplification.gfa
mgshot_S7938Nr1_metaspades3.15.5/assembly_graph_with_scaffolds.gfa
mgshot_S7938Nr1_metaspades3.15.5/strain_graph.gfa

Thanks in advance!

[Vini2]

Hi @GeoMicroSoares,

Thanks for your interest in Phables.

You should use assembly_graph_after_simplification.gfa for metaSPAdes assemblies.

Thanks!

[GeoMicroSoares]

Hi there - thanks for this! Just to make sure - I'm running one GFA and providing the corresponding reads file. When phables starts, it actually finds all my samples based on the prefix (as shown in phables.samples.tsv). Is phables running the GFA against all reads files, or just listing them and only taking the reads files with prefixes matching the input GFA?

[Vini2]

Hi @GeoMicroSoares,

phables runs the GFA against all the read files present in the provided input directory assuming it is a cross assembly. If you want to run one GFA file against its corresponding reads files, then you should have those corresponding reads files in a separate directory and provide it as input. I hope this clarifies things.

Thanks!

[Vini2]

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