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Old 11-07-2018, 02:47 AM   #2
Gopo
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Location: Louisiana

Join Date: Nov 2013
Posts: 38
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Code:
bwa index -a bwtsw genome.fasta
Code:
Usage:   bwa index [options] <in.fasta>

Options: -a STR    BWT construction algorithm: bwtsw or is [auto]
         -p STR    prefix of the index [same as fasta name]
         -b INT    block size for the bwtsw algorithm (effective with -a bwtsw) [10000000]
         -6        index files named as <in.fasta>.64.* instead of <in.fasta>.*

Warning: `-a bwtsw' does not work for short genomes, while `-a is' and
         `-a div' do not work not for long genomes.
You could also try BBMap as I have used it on the 32Gbp axolotl genome.
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