Sipprverse
What does it do?
Use Sipprverse to detect predefined or custom gene targets directly in raw or paired-end FASTQ reads. Sipprverse operates on unassembled read data; use GeneSeekr when the targets must be detected in FASTA-formatted assemblies. KMA can also analyze raw reads, but Sipprverse is the workflow intended for the supplied Sipprverse target analyses.
How do I use it?
Subject
In the Subject field, enter:
sipprverse
Spelling matters, but matching is not case-sensitive.
Description
The Description field must contain:
- an analysis declaration in the form
analysis=requested_analysis; and - one
SEQIDper line.
Example structure:
analysis=resfinder
2026-SEQ-0001
2026-SEQ-0002
Supported analyses
gdcs— detects genomically dispersed conserved sequences in Escherichia, Listeria, Salmonella, and Vibrio.genesippr— uses a custom suite of genes derived from Bacillus, Campylobacter, Escherichia, Listeria, Salmonella, Staphylococcus, and Vibrio.mash— finds the closest matching RefSeq genome.mlst— determines multilocus sequence type for Bacillus, Campylobacter, Escherichia, Listeria, Salmonella, Staphylococcus, and Vibrio.pointfinder— detects chromosomal mutations predictive of drug resistance.resfinder— identifies acquired antimicrobial-resistance genes.rmlst— determines ribosomal multilocus sequence type.serosippr— calculates the serotype for Escherichia.sixteens— determines the closest 16S match.virulence— detects virulence genes.full— runs all analyses listed above.custom— detects targets from a user-supplied FASTA file. This analysis requires an attachment.
Attachments
Most standard analyses do not require an attachment.
For analysis=custom, attach a FASTA-formatted file containing the target sequences.
Optional parameters
cutoff
Sets the minimum cutoff for matches included in a report.
- Default:
0.90 - Example:
cutoff=0.85
averagedepth
Sets the average pileup-depth cutoff.
- Default:
2 - Example:
averagedepth=3
kmersize
Sets the k-mer size used for baiting.
- Default:
19 - Example:
kmersize=11
Avoid lowering this value excessively. The supplied documentation recommends approximately 11 as the practical lower limit.
allowsoftclips
Controls whether hits containing internal soft clips are automatically discarded.
- Default:
False - Example:
allowsoftclips=True
Examples
Standard request
analysis=resfinder
2026-SEQ-0001
2026-SEQ-0002
See issue 15706 and issue 15707 for example Sipprverse issues.
Custom request
analysis=custom
2026-SEQ-0001
Attach the FASTA-formatted target file to the Redmine issue.
Interpreting results
When Sipprverse finishes, it uploads:
sipprverse_output.zip
The archive contains the reports generated for the selected analysis. Report contents vary by analysis.
How long does it take?
Runtime depends on the selected analysis, read volume, and number of requested SEQIDs. Because Sipprverse processes raw reads, expect a few minutes per SEQID.
What can go wrong?
A requested SEQID is unavailable
Symptom: The Redmine issue receives a warning identifying unavailable sequences.
Likely cause: Sipprverse cannot locate the raw paired-end FASTQ data for the requested SEQID.
What to do: Verify each SEQID and confirm that its raw paired-end reads are available.
The analysis is missing, misspelled, or unsupported
Symptom: The issue receives an error describing the requested analysis.
Likely cause: The Description omits analysis=..., contains a spelling error, or requests an unsupported analysis.
What to do: Choose one of the documented analysis names and submit a corrected request.
A custom target file is missing or unreadable
Symptom: The custom analysis cannot read or use its target database.
Likely cause: The FASTA-formatted target file was not attached or could not be read.
What to do: Attach a valid FASTA-formatted target file and submit a corrected analysis=custom request.