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andrewjpage / krocus

Predict MLST directly from uncorrected long reads
GNU General Public License v3.0
25 stars 6 forks source link

Tool output questions #2

Closed Karhide closed 6 years ago

Karhide commented 6 years ago

Hi there!

I gave your tool a spin recently (latest version) and just had a few questions, possibly leading to updated documentation.

  1. What do the asterisks mean, e.g. gmk(319)* ?
  2. Why do I see multiple of the same MLST profiles identified? E.g.: Novel tpi(216) gmk(319) yqiL(182) arcC(46) glpF(223) aroE(484) pta(131) Novel tpi(216) gmk(319) yqiL(182) arcC(46) glpF(223) aroE(484) pta(131)

I have a feeling these might be dumb questions, so thanks in advance!

andrewjpage commented 6 years ago

Thanks for testing it out. I'll have to add some documentation!

By default every X number of reads it will print out the current predicted MLST profile. You can set it to just print everything out at the end after processing all reads. The idea is that you can stop it running when a consistent result pops out (e.g. if you are running it in real time while sequencing on a minION). The star indicates a partial match.

Andrew

On 15 February 2018 at 15:02, Karhide notifications@github.com wrote:

Hi there!

I gave your tool a spin recently (latest version) and just had a few questions, possibly leading to updated documentation.

  1. What do the asterisks mean, e.g. gmk(319)* ?
  2. Why do I see multiple of the same MLST profiles identified? E.g.: Novel tpi(216) gmk(319) yqiL(182) arcC(46) glpF(223) aroE(484) pta(131) Novel tpi(216) gmk(319) yqiL(182) arcC(46) glpF(223) aroE(484) pta(131)

I have a feeling these might be dumb questions, so thanks in advance!

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Karhide commented 6 years ago

Thanks for the clarification, everything makes sense now, as expected I was being a numpty!