Question about --trusted-contigs

[fciamponi]

Hello SPAdes team!

First, I'd like to congratulate you on an amazing work. However, I'd like some clarification of one particular option from the assembler, specifically the --trusted-contigs entry.

From the manual, it says:

Additional contigs
In case you have contigs of the same genome generated by different assembler(s), and you wish to add them into SPAdes assembly, you can specify additional contigs using --trusted-contigs or --untrusted-contigs. The first option is used when high quality contigs are available. These contigs will be used for graph construction, gap closure and repeat resolution. The second option is either used for less reliable contigs, which may have more errors, or for contigs of unknown quality. Such contigs will be used only for gap closure and repeat resolution.

Both options allow providing unlimited number of contigs.

Note, that SPAdes does not perform assembly using genomes of closely-related species. Only contigs of the same genome should be provided.

What if instead of a closely-related species, I'd like to use the reference genome of the species I'm working with? In my case, I'm assembling the genome of several bacillus isolates from the same species... could I use the available NCBI RefSeq assembly to improve the quality of my assembly?

I've ran some tests with and without this option and the differeence between them is negligible... so this is more of a "am I using this right?" question as opposed to something crucial to our work.

Thanks for the assistance!

[asl]

I've ran some tests with and without this option and the differeence between them is negligible... so this is more of a "am I using this right?" question as opposed to something crucial to our work.

Well, is there are no differences in the results, then likely not. SPAdes does not perform reference-assisted assembly, if you're doing this you can easily have a frankenstein results containing both sequences from your input and from reference genome. It's unlikely you'd want this. Anyway, there must be differences in you're providing a complete reference genome. Can you post your spades.log with and without here?

[fciamponi]

Sure, here is the spades logs for both runs, as well as quast and busco outputs. In case it is relevant, this is data from benchmark known BT isolate we usually use for control in our experiments.

quast_results.zip
short_summary.specific.bacillus_odb12.05-Isolate_Trusted.txt
short_summary.specific.bacillus_odb12.04-Isolate_Only.txt
spades_isolate_trusted.txt
spades_isolate.txt