I have paired-end fastq files, however my reference genome is in a list of contigs. Thus, the referece fasta file looks something like this
>contig1 AGTGCAGAC..... >contig2 GCGATCACA...... >contig3 ....
Is there a way to instruct
bwa to perform alignement on the 'contig1', then move on the 'contig2' and so on? Concatenating contrigs into one single fasta file is not an option as I'll have random pairing of contigs and paired-end reads might be mapped to different contigs producing all sorts of funny stuff.
I tried looking for this on previous posts but couldn't find anything similar.