Hello all,
I am looking to use BBNorm to normalize my sequencing data to a read depth of 60X coverage before using Discovar DeNovo to assemble it into a reference genome. I have already assembled two references using all of my 8 sample sites (pools of 40 individuals) and one with 3 of what I predict will be the most closely related sites (post clumpify.sh to remove duplicates) but am looking to improve the assembly.
I have concatenated all 8 sites and just the 3 into R1 and R2 files and ran the below:
bbnorm.sh in=all_R1.fq.gz in2=all_R2.fq.gz out=all_R1_bbnorm.fq.gz out2=all_R2_bbnorm.fq.gz outt=getridof hist=kmer_hist target=60 maxdepth=70 mindepth=5 threads=32
However, it normalized it to the default of 100? Is there an issue with the above? As well, I am not sure what to set the mindepth to or what other options I should select. I have read the manual and other posts, however still feel unsure as to what would be appropriate. Any help is greatly appreciated!
Thank you, Brenna
