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snippy (version 4.6.0+galaxy0)
Built-ins were indexed using default options. See `Indexes` section of help below. If you would like to perform self-mapping select `history` here, then choose your input file as reference.
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Select between paired and single end data
Specify dataset with forward reads
Specify dataset with reverse reads
Advanced parameters
Advanced parameters 0

Snippy @VERSION@

Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels).


Torsten Seemann


  • NGS Reads in fastq format (single or paired end)
  • Reference file in either fasta or genbank format

If the reference file is supplied in genbank format, snpeff will be called to determine the effect of any snps found.

Advanced options

  • mapping quality - Integer - Minimum mapping quality to allow (default '60')
  • minimum coverage - Integer - Minimum coverage of variant site (default '10')
  • minimum fraction - Float - Minumum proportion for variant evidence (default '0.9')
  • minimum quality - Float - Minumum QUALITY in VCF column 6 (default '100.0')
  • rgid - String - Use this @RG ID: in the BAM header (default '')
  • bwaopt - Extra BWA MEM options, eg. -x pacbio (default '')

Further information

For a much more in depth description of snippy and how it works, see