Geneious has the wonderful possibility to sort blast hits into two bins, hit or no-hit. This is quite useful to i.e. separate metagenomes (i.e. host reads vs. endosymbiont reads). While Geneious works very well with smaller data-sets on a local computer, for large data-sets you need a lot of patience. Is there any way to use a command line blast in the same way so one ends up with two files with the sequence IDs or even better two files with hit vs no-hit sequences? There is no need at all to produce all that alignments.
I thought about a similar approach with BBMap, but because in our case there is no reference genome from the same species blasting the hits against a somewhat related genome might be the better approach.
Thank you for your help, JD