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 default 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 running on 1 core and 1GB of memory, to predict squiggles:
#!/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