DiscoSnp++ is an efficient tool for detecting SNPs without a reference genome.

discosnp_pp

Version	Tool Shed	Owner	Galaxy instances where the tool is available
2.5.4+galaxy0	toolshed.g2.bx.psu.edu	iuc	galaxy.genouest.org
2.5.4	toolshed.g2.bx.psu.edu	iuc	galaxy.genouest.org
2.3.0	toolshed.g2.bx.psu.edu	iuc	bipaa-galaxy.genouest.org
2.3.0	toolshed.g2.bx.psu.edu	iuc	galaxy.genouest.org
2.2.10	toolshed.g2.bx.psu.edu	iuc	galaxy.genouest.org