Hi,
I am working with 2 different bacterial samples with 1 being very high in GC-rich content while other being sinilar to humans. I have mixed these samples in equal amounts and performed WGS experiment. I have 2 questions:
1). What is the best aligner to use for prokaryotic genomes? I have most often used bowtie but is there a better one or recommended one for prokaryotic genomes?
2). From what I have read in other galaxy chats, people have recommended concatenatung reference genomes of the 2 bacterial specias and using this combined reference genomes? What would be best practice here? Also, I am not doing variant calling with these datasets, i am simply collecting some nga lobrary quality metrics ?
I would really apprecaite any help or advice on this.
Thank you.