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🌺 Short pipeline for counting number of clusters across .sam files

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Project-cluster

Identify and count clusters across a series of .sam files.

Usage

python run.py --help

Install

git clone https://github.com/DomBennett/Project-cluster.git

Or download the zipped folder:

wget https://github.com/DomBennett/Project-cluster/archive/master.zip

Requirements

  • One .sam file stored per folder
  • cdhit
  • Python (v2 or v3)

Steps

  • Convert .sam to .fasta by extracting the orthologous sequence identified within the .sam file.
  • Run cdhit
  • Count clusters with greater than min_nsqs
  • Report number of clusters per .sam in a .csv

Authors

D.J. Bennett & J.S. Eriksson

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🌺 Short pipeline for counting number of clusters across .sam files

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