I would like to find the variants among two different genomes (both are paired end reads). I removed the low quality reads for two genomes using sickle tool. Now i got two paired end output files from sickle which are in fastq.gz format. Can anyone suggest me the tool for aligningtwo different genomes. I am searching for an option in bwa but i did not find it.. or can i concatenate paired end fastq files of one genome into one file and then convert it to fasta file to create an index file.