|Snippy finds variants between a haploid reference genome and your NGS sequence reads. It will find both substitutions and insertions/deletions (indels).
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/snippy
|Minimum Galaxy Version
|Snippy finds SNPs between a haploid reference genome and your NGS sequence reads.
|Replace any non-standard sequence characters in snippy 'core.full.aln' file.
|Combine multiple Snippy outputs into a core SNP alignment