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Supernova

Supernova is a software package genome assembly from Chromium Linked-Reads that are made from a single whole-genome library from an individual DNA source.

Supernova is available as a module on Apocrita.

Usage

To run the latest installed version of Supernova, simply load the supernova module:

$ module load supernova
$ supernova --help

Usage:
    supernova mkfastq
    supernova run
    supernova mkoutput
    supernova testrun

For more information regarding each analysis pipeline, pass the --help switch after the pipeline sub-command (i.e. supernova run --help).

Example job

Serial job

Here is an example job running on 4 cores and 16G total memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 4
#$ -l h_rt=1:0:0
#$ -l h_vmem=4G

module load supernova

supernova run --id 1234 \
              --fastqs raw_data.fastq \
              --sample 1234 \
              --disable-ui \
              --localcores ${NSLOTS} \
              --localmem 16

Reference