Output files when MismatchCorrector is enabled

[sallesmath]

Question

Hi!

I just ran SPAdes with the MismatchCorrector option enabled (--carefull option).

And now I have three files with assembled contigs. Could you tell me if they are the same, or do they correspond to different assemblies?

These are the files I'm talking about:

1. 'contigs.fasta' file, located on the first page of the results folder
2. 'assembled_contigs' file, located in the 'misc' folder
3. 'corrected_contigs' file, located in the /mismatch_corrector/contigs folder

Thanks!

spades.log

spades.log

params.txt

params.txt

SPAdes version

SPAdes 3.15.4

Operating System

Linux-5.4.72-microsoft-standard-WSL2-x86_64

Python Version

2.7.16

Method of SPAdes installation

manual

No errors reported in spades.log

• Yes

[asl]

Hello

The log clearly reads:

 * Corrected reads are in /home/sallesmath/dados_uce/phyluce_dados_uce_tropidurus/dados_andre/spades-assemblies/new_test_amcc204364_spades/corrected/
 * Assembled contigs are in /home/sallesmath/dados_uce/phyluce_dados_uce_tropidurus/dados_andre/spades-assemblies/new_test_amcc204364_spades/contigs.fasta
 * Assembled scaffolds are in /home/sallesmath/dados_uce/phyluce_dados_uce_tropidurus/dados_andre/spades-assemblies/new_test_amcc204364_spades/scaffolds.fasta
 * Paths in the assembly graph corresponding to the contigs are in /home/sallesmath/dados_uce/phyluce_dados_uce_tropidurus/dados_andre/spades-assemblies/new_test_amcc204364_spades/contigs.paths
 * Paths in the assembly graph corresponding to the scaffolds are in /home/sallesmath/dados_uce/phyluce_dados_uce_tropidurus/dados_andre/spades-assemblies/new_test_amcc204364_spades/scaffolds.paths
 * Assembly graph is in /home/sallesmath/dados_uce/phyluce_dados_uce_tropidurus/dados_andre/spades-assemblies/new_test_amcc204364_spades/assembly_graph.fastg
 * Assembly graph in GFA format is in /home/sallesmath/dados_uce/phyluce_dados_uce_tropidurus/dados_andre/spades-assemblies/new_test_amcc204364_spades/assembly_graph_with_scaffolds.gfa

Hope this helps. SPAdes manual (https://cab.spbu.ru/files/release3.15.4/manual.html#spadesoutput) contains more information about SPAdes output

[sallesmath]

I apologize, but I'm still confused. As a post processing tool, MismatchCorrector is not acting on the resulting contigs?

That 'new_test_amcc204364_spades/corrected/' folder only contains corrected reads, not contigs.

Anyway, is there no difference between the files I mentioned earlier? See below:

1. 'contigs.fasta' file, located on the first page of the results folder
2. 'assembled_contigs.fasta' file, located in the 'misc' folder
3. 'corrected_contigs.fasta' file, located in the /mismatch_corrector/contigs folder

My question is whether these three files have the same content or not. I didn't find this information in the manual.

Thanks again!

[asl]

Your output is as follows:

* Assembled contigs are in /home/sallesmath/dados_uce/phyluce_dados_uce_tropidurus/dados_andre/spades-assemblies/new_test_amcc204364_spades/contigs.fasta
* Assembled scaffolds are in /home/sallesmath/dados_uce/phyluce_dados_uce_tropidurus/dados_andre/spades-assemblies/new_test_amcc204364_spades/scaffolds.fasta

Everything else are internal assembler files and not intended for any external usage.

[sallesmath]

Got it.

Thanks a lot.