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Python API for cortex.

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Python API for cortex.


pip3 install git+


R and python 2 are required.

sudo apt install r-base-core python2.7


Inputs: * a reference genome in fasta[.gz] * one or more reads file in fasta/q[.gz]

Use a list to pass in reads files, even if there is only one file.

Output: A vcf with variants detected by cortex.

import cortex.calls as cortex"./reference.fasta",

The third argument is where to place the output vcf.


The following options can be passed to

  • sample_name: sample name to appear in output vcf (default: 'sample').
  • ploidy: 1 or 2, for haploid or diploid genotyping (default: 1)
  • mem_height: if cortex.calls fails warning of too low memory, use a higher value (default: 22).
  • tmp_directory: where to place intermediate output and log files (default: system-defined)
  • cleanup: whether to remove intermediate output and log files upon successful completion. (Default: True)



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