How To Remove Contaminated Scaffold From Genome

Question

[raj.gzra]

hi everyone i have a fungal genome and i want to know that if anybody know, how to remove contaminated scaffolds from genome. if i do BLAST my genome sequences with contaminated species genome and i found hits. anybody know that, on what basis i have to remove that hits from my scaffold or i have to remove whole contaminated sequence or only some part of scaffold if it is contaminated. thank you

[Pavel Senin]

Did you assemble the genome by yourself? If so, then the easiest way will be to roll back a bit - remove the reads which hit contaminants and to reassemble.

[raj.gzra]

no i did not assemble. i got assembled genome. do you know how to remove contaminated scaffold ?

[Pavel Senin]

if it's a multi-fasta file, you just cut it off from it. now, it is not really clear what sort of hits you have - i.e. what is the evidence that it is contaminated. If I were you, I would look on the synteny map (see example) to make a decision about cutting off the whole scaffold or its part.