Dear all, I posted a similar topic recently. I have a few draft genome data, all of which contain roughly 12 million 88 bp reads. I also have ~200 genes from reference organism, and need to find homologous sequences from the draft genomes. What's your ideas regarding to the order of assemble and BLAST? Assemble draft genomes and then perform BLAST or BLAST before assemble? Personally i prefere the latter approach for two reasons. Frist, the reads are 88 bp in lenght that is suitable for BLAST. Extracting the homologous reads is easy. Second, I only need to find 200 genes' homologs, so assembling genomes seems time-consuming. What's your ideas and what you suggest? Both methods are OK? THANKS A LOT!