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BIT 815, Deep Sequencing Data Analysis

Using the HPC for Bioinformatics Computing

Global overview

  1. Accounts on the HPC are available to those with an NCSU Unity ID - see HPC Accounts for information.
  2. Connect to the HPC via login64.hpc.ncsu.edu using PuTTY for a command-line interface
  3. Create a job submission script file that contains the commands you want to execute
  4. Submit the job script to the appropriate queue and wait until the job is complete
  5. Transfer the output data back to your office workstation for further analysis, or write another job submission script to carry out more analysis on the HPC.

Job submission and management

A tool called Load Sharing Facility (LSF) is used to manage the queues of submitted computing jobs on the HPC cluster. See LSF on HPC Cluster for a summary of the factors considering in prioritizing submitted jobs in the queue. More information is available at the FAQ for HPC users; additional documentation on LSF commands can also be found via Google searches, e.g. LSF Basics at Stanford University.

Available software

The most current list of software available on the HPC can be obtained by logging into the HPC and listing the contents of the directory /usr/local/apps. As of mid-November, 2013, installed software useful for biological research applications included a mix of open-source and commercial tools:
abyss-1.0.14
asreml2
BEAST.v1.4.7
bowtie
bwa
circos
cufflinks
cutadapt
EIGENSOFT-3.0
exonerate
FastQC
fastx_toolkit
java
maker
maq
mpiblast-1.4.0
mrbayes-3.1.1
mrbayes-3.1.2
MUMmer
ncbi-blast
ncbi-em64t
ncbi-sra
oases
octave-2.1.73
paup4b10-x86-linux-icc
paup4b10-x86-linux-icc.orig
paup4b10-x86-linux
paup4b10
perl, bioperl
plink
python-2.6.5
python-2.4.4
R-2.3.1
raxml
RepeatMasker
samtools
sparsehash-1.5.2
spss
SQLite
sqlite
stacks
tassel
tophat
trinity
velvet

Setting up a job submission script

  • Using GemSIM to create simulated datasets of reads with different insert size and end orientation - download GemSIM.sh script here.

    Submitting to the HPC