Removing reads from data using Blast

Question

[Bioinfo]

Hello everyone

please i have a question

my data is contaminated by a host dna and i want to remove all the reads that correspond to host dna using blast

can anyone tell me please how can i do that ?

Thank you very much

[Ram]

my data is contaminated by host DNA

You mean like in a xenograft, where host and graft cells get mixed up before sequencing? If not, how did the contamination happen?

I think you should be able to use BBSplit to separate reads from multiple organisms if you have the reference genome for each organism involved.

[Bioinfo]

because i want to do assembly of endosymbiotic bacteria and it's probably contaminated by host mitochondrial dna

Answer 1

[GenoMax]

If you have fastq data then the best way to do this is use bbsplit.sh from BBMap suite to bin your reads. Read more about it here.