Hi,
I would like to check for contaminants using both phiX and the human genome. My data is metagenomics data and i want to remove any read mapping to both phiX and the Human genome.
So far bbduk can handle this by using the ref=phiX.fa
However for checking contaminations from human samples i would like to ust the non redundant nucleotide database. It is split into small pieces and usually i access them through blast using the reference nt.nal file.
Is that is also feasible with bbduk ??
I would like to check for contaminants using both phiX and the human genome. My data is metagenomics data and i want to remove any read mapping to both phiX and the Human genome.
So far bbduk can handle this by using the ref=phiX.fa
However for checking contaminations from human samples i would like to ust the non redundant nucleotide database. It is split into small pieces and usually i access them through blast using the reference nt.nal file.
Is that is also feasible with bbduk ??
Comment