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snippy (version 0.2.0)

Reference type:

File type of the reference file. (Fasta or Genbank)

Reference Genbank:

Genbank file to use as the reference

Single or Paired-end reads:

Select between paired and single end data

Select first set of reads:

Specify dataset with forward reads

Select second set of reads:

Specify dataset with reverse reads

Cleanup the non-snp output files:

Remove all non-SNP files: BAMs, indices etc

Advanced parameters:

unhide advanced parameter settings

Synopsis:

snippy 3.0 - fast bacterial variant calling from NGS reads

Author:

Torsten Seemann <torsten.seemann@gmail.com>

Usage:

snippy [options] --outdir <dir> --ref <ref> --pe1 <R1.fq.gz> --pe2 <R2.fq.gz>

snippy [options] --outdir <dir> --ref <ref> --se <454.fastq>

snippy [options] --outdir <dir> --ref <ref> --peil <velvet.fa.gz>

Options:

`--help`	This help
`--version`	Print version and exit
`--citation`	Print citation for referencing snippy
`--quiet`	No screen output (default OFF)

--cpus [N] Maximum number of CPU cores to use (default '8')

--reference [X] Reference genome. Supports FASTA, GenBank, EMBL (not GFF) (default '')

--outdir [X] Output folder (default '')

--prefix [X] Prefix for output files (default 'snps')

--force

Force overwrite of existing output folder (default OFF)

--pe1|R1|left [X] Reads, paired-end R1 (left) (default '')

--pe2|R2|right [X] Reads, paired-end R2 (right) (default '')

--se|single [X] Single-end reads (default '')

--peil [X] Reads, paired-end R1/R2 interleaved (default '')

--mapqual [n.n] Minimum mapping quality to allow (default '60')

--mincov [N] Minimum coverage of variant site (default '10')

--minfrac [n.n] Minumum proportion for variant evidence (default '0.9')

`--report`	Produce long report with visual alignment (slow) (default OFF)
`--cleanup`	Remove all non-SNP files: BAMs, indices etc (default OFF)

--rgid [X] Use this @RG ID: in the BAM header (default '')

--bwaopt [X] Extra BWA MEM options, eg. -x pacbio (default '')