Aligning whole genome (FASTA) to reference genome

[mmsa22]

Hello all,

I previously aligned several fastq files (sample.merged.dedup.realn.bam) to a reference genome using bwa-mem.
Now I want to align a different species sample to the same reference genome, but this file is a whole genome sequence in fasta format.

I found this thread: http://seqanswers.com/forums/showthread.php?t=35608

Which made me tempted to use bowtie2 like this:

bowtie2 -p 4 -f -x reference -U genome.fasta -S genome.aligned.sam

However I'm not sure I can do this or if I should try using a different tool/method.
After aligning and converting to bam format, I want to do variant calling for the whole dataset.

Thank you in advance,
Maria

[colindaven]

I think it would be better to use minimap2 with the asm5 asm10 asm20 settings, see

Preset:
-x STR preset (always applied before other options; see minimap2.1 for details) []
- map-pb/map-ont: PacBio/Nanopore vs reference mapping
- ava-pb/ava-ont: PacBio/Nanopore read overlap
- asm5/asm10/asm20: asm-to-ref mapping, for ~0.1/1/5% sequence divergence
- splice: long-read spliced alignment
- sr: genomic short-read mapping