tseemann/mlst

Title fight: mlst vs cge

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#102 opened on Mar 19, 2021

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Description

Trying to understand a discrepancy between my much loved mlst vs CGE webtool (https://cge.cbs.dtu.dk/services/).
I have an isolate of S.suis, sequenced with Illumina > denovo assembled contigs generated with unicycler. I am getting 100% match on an allele with CGE (mutS_408) but in mlst I am getting "novel" allele (mutS_317). When I take that novel allele output and run through CGE i get 100% match to CGE allele (mutS_408).

All inputs for mlst are default except for --novel and --csv flags.

Just trying to figure out where i might be generating errors.

love your work, thank you for maintaining mlst.

Contributor guide

Research direction
Compare the novel allele sequence reported by mlst against the CGE database to identify discrepancies. Verify the reference sequences used by both tools.
Tech stack
perl
Domain
data
Issue type
Bug
DifficultyEstimated implementation difficulty for a new contributor, from 1 for very small changes to 5 for expert-level work.
2
Estimated timeA rough time range for an experienced contributor to investigate, implement, test, and prepare a pull request.
1-3 hours
Activity statusHow available the issue appears right now: fresh, active, stale, blocked, or waiting on maintainer input.
Active
ClarityHow clearly the issue explains the expected change, acceptance criteria, and next step.
Clear
Prerequisites
None
Newbie friendlinessA 1-100 score estimating how approachable this issue is for first-time contributors.
50