I have illumina paired-end whole-genome sequencing reads which I have map to around -400 reference plastid genomes. After getting mapped reads, I have to assemble as de novo plastid genome.
1. Do I have map reads to invidiual reference genomes one by one, or can I download all genomes at one go and index as one reference genome?. Do bwa or bowtie has
enough memory to index 400 genomes as one reference index genome?
2. Do you think which one is best method?. Mapping individual genome or all genomes indexed as one?
3. If I have to map individually, can I combine all bam file together and Can I convert to fastq file using bam2fastq tool (in picard) for denovo assembly?