Hi,
I have 9 genomes, I would like to produce a metagenome like distribution using randomreads.sh. I concatenated genome fasta files in one reference file. Then, ran as below.
../bbmap/randomreads.sh ref=simplified_catgenome.fasta out1=20M.read1.fastq out2=20M.read2.fastq length=125 paired=t metagenome=t genome=9 reads=20000000
However, I would like to know if there is any way I can define the abundances for each genome based on qPCR results and then produce the reads accordingly. Would there be a way to produce reads from each genome separately with the absolute abundances?
Thank you!
Can you not generate the reads independently and mix them as needed? You can then use
shuffle.sh
to mix the reads randomly giving you a representative metagenome.I can generate the reads independently. But does shuffle.sh have a function of indicating the abundances? I didnt see any!
I was thinking that you would add known amounts of reads together based on your needs and then simply shuffle them so they represent a mixed metagenome.
Thats my question! How do I add known amount of reads? I will produce randomreads.sh from each genome, then shuffle them , right? But in which step exactly I am adding the known amount of reads for each genome.