I need an advice to how reduce the depth of a sequencing, because when I used the workflow and I had a huge bacterial genome of more than 10000 genes for a genome usually of 6000 genes. This organism was sequenced with Illumina MiSeq, the reads were 300 nt (2x300) so R1 was 1,873,799 and R2 1,873,799.I calculated the coverage was approximately 224x.
I need to reduce it to 100x or near of it. I used trimmomatic and spades to work it. I'm open to any software or tool to have it done. Thank you!