Synthetic construct and cloning vector contamination in scaffolds

Question

[Bio22]

Hi folks,

As a beginner, I am still not familiar with the roles of this amazing and informative community, so sorry if I could not introduce my question in a proper way.

I got Illumina high seq reads of bacterial isolate, removed adapters and low quality reads using trimmomatic, and performed the assembly using spades, then scaffolding using MEDUSA platform, with several references. I then used NCBI VecScreen, to see whether I have contamination. The screening results showed me possible Synthetic construct and cloning vector contamination in my scaffolds.

I am wondering whether we can trust VecScreen!, and is there any pipeline or software to remove this contamination!!!

[GenoMax]

If you just did a standard Illumina library it seems unlikely that there will be a vector contaminating the assembly. Are those cross hits coming from plasmid(s) your bacteria had that may be leading to these false positive hits with VecScreen?

[Bio22]

Hi @genomax

The library (NexteraXT ) was prepared by the sequencing company. Adapters were removed in previous step... I checked my scaffolds using ( PlasmidFinder-2.0 Server), because I thought as you mentioned, may they are just bacteria endogenous plasmids. However, Plasmidfinder showed me no hits = no plasmids.

I am confused because In my project I sequenced 2 bacteria at the same time, same process. while this one showed me this contamination, the second one' scaffolds were clean !!