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Misc utility scripts

Misc scripts

  • trim-noV.sh - a script to do trimming of short reads. requires khmer >= 2.0.

Debugging and testing scripts

  • check-tree.py - exhaustively confirm the results of a search on an SBT.
  • compute-dna-mh-another-way.py - a separate implementation of MinHash signature calculation for DNA.
  • compute-input-prot-another-way.py - a separate implementation of MinHash signature calculation for proteins.
  • compute-prot-mh-another-way.py - a separate implementation of MinHash signature computing for 6-frame translations of DNA into amino acid space.

CTB 1/2019

Formula implementations

  • cardinality_estimate_confidence.py - a function that will tell you if the sketch size is too small to trust the estimate sketch_size * scale as an estimate of the number of distinct k-mers.

DMK 5/2022