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!!!