I would be interested in mapping reads to complete bacterial genomes using bwa-sw or Bowtie2. But I'm unable to index the complete genome file (single FASTA with all bacterial genomes from NCBI) using BWA/Bowtie2 as it reports error on the limit of sequence bases in the reference file.

Can anyone suggest me what is the best approach to accomplish this? I'm not interested in splitting the sequences in 3-4 chunks and created multiple index files, as it would be difficult to extract unmapped reads .

Pl suggest