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Scrappie

Scrappie has been written by the Oxford Nanopore Technologies Research Algorithms group to demonstrate the next generation of base calling.

Scrappie is available as a module on Apocrita.

Usage

AVX2 instruction set required

Scrappie requires the AVX2 instruction set. To guarantee a job will run on nodes which support AVX2, pass the -l avx2 parameter in the job script. See the node types page for a table of supported CPU instruction sets per node.

To run the latest installed version of Scrappie, simply load the scrappie module:

module load scrappie

For usage documentation, run scrappie help [program].

Example job

Serial job

Here is an example job to predict squiggles, running on 1 core and 1GB of memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G
#$ -l avx2

module load scrappie
scrappie --output=squiggle.out input.fa

Reference