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1. Pipeline and program descriptions

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Eve Zeyl Fiskebeck edited this page Feb 21, 2025 · 2 revisions

test

Software

Our pipeline wrangles the results of NucDiff to table format in a databse so they can be used for statistical analyses. Annotation ...

NucDiff : in-depth characterisation and annotation of differences between two sets of DNA sequences

NucDiff is the software that allow to detect differences between pairs of isolates. It detects

  • "Global" differences (eg. sequences that do not exist in one of isolate pair under comparison)
  • "Local" differences: Different types of Insertions, deletions and Substitutions
  • "Structural" differences: reshudling, inversions, relocation / translocations.

Be aware that with draft genomes, different assemblies (eg. different methods) can produce apparent differences that do not actually exist. This, because assemblies are a model of the real genome sequences, and are unperfect (eg. missassemblies).

We refer to NucDiff manual and publication for in detail information.

Links:

DBscript

Wrangles the results from NucDiff (gff3 files) and ... into tables so they can be used for statistical analyses.

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