Does spades/metaspades normally having missing nodes?

Question

[DNAngel]

Hello experts,

Just wondering if it is a common thing that my contigs.fasta file is missing nodes. For example, I will have nodes 1-100, but as I get into higher numbers I will be missing some so I will have node_110, node_111, node_115. Where is node_112, node_113, and node_114?

Thank you!

Answer 1

[lieven.sterck]

without knowing the details I fear you might be over-thinking this.

It is very well possible the assembly algorithm made some sort of initial "nodes" and later in the process merged them with other or simply eliminated them because they turned out not useful or wrong.

I would personally not worry about this, spades is a well tested frequently used software (it's not some obscure perl or python script you dug up somewhere), if anything serious would be wrong with it, people would likely have notice it already.

Do you have reasons to think you might be missing things from the assembly? Did you got any errors or warning during the process that made you think so?

[DNAngel]

I just found out by digging more into my output files from metaspades. It was not an issue with metaspades it was actually an issue with my blast. The contigs.fasta file when using grep -c "NODE" returns the same number of lines as my input fasta file. When grepping for certain number ranges, all numbers are there. My blast result file (after blasting my contigs with blast+) was missing reads and I think it may be due to time limits or thresholds I set. I have to confirm this though by rerunning it but the contigs.fasta file and even the first_pe_contigs.fasta file had all the numbers there!