Diamond and Taxonomic information

Question

[emiliomastriani]

Hello, I successfully executed the diamond makedb and blastx processes, and obtained the data file containing also the taxonomic information. Of course, I ran the makedb in the correct way, including the needed files:

diamond makedb -p 4 --in /storage/RefSeq/small.nonredundant_protein.faa --taxonmap /storage/RefSeq/prot.accession2taxid --taxonnames /storage/RefSeq/names
.dmp --taxonnodes /storage/RefSeq/nodes.dmp -d refseq_protein_nonredund_diamond -v --log

And I also checked if the daa file contains all the information:

emastriani@gandalf:~/MetaVic/TestSmallDiam$ diamond view --daa blastx_diamond.daa | head
SRR957824.5 WP_048289503.1  72.9    48  13  0   1   144 61  108 3.60e-21    83.6
SRR957824.5 WP_043875529.1  67.4    46  15  0   139 2   87  132 2.45e-15    68.6
SRR957824.8 WP_047660053.1  78.0    50  11  0   150 1   394 443 1.46e-21    89.4
SRR957824.8 WP_047660053.1  86.4    44  6   0   3   134 368 411 9.51e-23    92.4
SRR957824.10    WP_102803206.1  92.6    27  2   0   81  1   28  54  2.17e-11    58.9

Also with the output format option -f 6 qseqid staxids evalue

emastriani@gandalf:~/MetaVic/TestSmallDiam$ head blastx_diamond
SRR957824.5 573 3.60e-21
SRR957824.5 570 2.45e-15
SRR957824.8 562 1.46e-21
SRR957824.8 562 9.10e-23
SRR957824.10    1134687 2.17e-11
SRR957824.10    671990  9.78e-13
SRR957824.12    208962  1.33e-20
SRR957824.12    208962  2.69e-24
SRR957824.15    53410   1.94e-04
SRR957824.16    562 3.48e-12

So, the daa output db seems to be correct. My question is: how can I browse the obtained results? It looks that the standard way is using MEGAN to make the taxonomic step and browse the results, but I don't want to repeat the taxonomic step. I could use the f6 output file to parse the results, but it's a little bit boring because I need to focus only on viruses, environmental and unknown sequences from my data. Any suggest? Thank you.

Answer 1

[Istvan Albert]

I would recommend that you use methods you are already familiar with, like MEGAN,

in general, most tools require you to have the data in a specific format, thus it is likely you would need to rerun the alignment to match what the programs require, thus there is likely no way around that.

You might also want to investigate other tools like:

• KRONA: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-385
• BLASTGrabber: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-128
• BlasterJS: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0205286

and there may be many other alternatives