Hi all,

Through the WGS analysis process of my illumina high-seq reads (bacteria), I used NCBI Vecscreen tool, to remove the possible contamination.

results of the vec-screening showed me :

Strong match: 43133-43183, 125079-125855, 127487-128489, 584484-585566, 1801604-1802631, 2193142-2195079, 2272081-2273056, 2682705-2684037, 2781633-2782735, 3002888-3003126, 3178028-3179024, 3363408-3365414, 4012933-4013051, 4013635-4013930, 4045120-4045162

Moderate match: 341490-341524, 4012627-4012703

Weak match: 3851592-3851621, 4013428-4013480

My questions:

1- Is it usual to get such high contamination, although I removed all adapters and low quality reads in a previous step (trim-galore)!!

2-should I remove all strong-moderate-weak matched sequences!!

3- What tool is recommended to remove this contamination !!!

Thanks for your time