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Published September 11, 2023 | Version v1.3.0
Software Open

JannesSP/magnipore: v1.3.0

Authors/Creators

  • 1. Friedrich Schiller University Jena

Description

Changed
  • the 7mer context for r9 to a 5mer context
    • some data showed significant signals near a mutation that are within a 7mer context, but not a 5mer context - hard to say if from mutation or not (no proof). Therefore, stick to the number of nucleotides measured together depending on the pore-type.
  • MeanDiffAvgStdDev plots are now called MeDAS, meaning Mean Distance Average Standard-deviation
    • MeDAS plots showing the coverage
    • plots are now created using the magniplot.py
    • before: created with magnipore.py
  • change part of logger file name created by the subscript nanocherlock.py from "magnipore" to "nanosherlock"
  • gzip will now overwrite already existing output files
Added
  • different ranges for the classification of a significant signal into mutation or potential modification depending on the pore type
    • r9: 5mer context
    • r10: 9mer context
  • magnifilter.py: a script to filter the given .magnipore output file for a given coverage threshold
  • magnicheck.py: a script to check if magnipore found the positions in a context of given validated ground truth positions
  • multiprocessing of magnipore model comparisons

Files

JannesSP/magnipore-v1.3.0.zip

Files (2.6 MB)

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md5:1ea20e5c344bb180c20f5db326dc3163
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Additional details

Related works

Is supplement to
https://github.com/JannesSP/magnipore/tree/v1.3.0 (URL)