HPC – Lampredi – software update – LoFreq 0.6.1

Feb 242014

LoFreq 0.6.1 was added to the cluster (05/12/2013)

A fast and sensitive variant-caller for inferring single-nucleotide variants (SNVs) from high-throughput sequencing data.

http://sourceforge.net/p/lofreq/wiki/Home/
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$ module load apps/lofreq
apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3
| — libs/gcc/system
| * –> OK
| — apps/python/2.7.3/gcc-4.4.6
| | — libs/gcc/system … SKIPPED (already loaded)
| * –> OK
|
OK

$ ls $LOFREQDIR
bin python

$ ls $LOFREQBIN
base_qual_calib_wrapper.sh lofreq_bonf.py lofreq_pileup_summary.py lofreq_snpcaller.py lofreq_varpos_to_vcf.py
bwa_unique.sh lofreq_diff.py lofreq_regionbed.py lofreq_uniq_pipeline.py lofreq_version.py
lofreq_alnoffset.py lofreq_filter.py lofreq_samtools lofreq_uniq.py

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$ module whatis apps/lofreq
apps/lofreq :

Title: LoFreq
Summary: fast and sensitive variant-caller for inferring SNVs from high-throughput sequencing data
License: BSD License
Group: Bioinformatics
URL: http://sourceforge.net/p/lofreq/wiki/Home/

Name: lofreq
Version: 0.6.1
Module: apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3
Module path: /opt/gridware/etc/modules/apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3
Package path: /opt/gridware/pkg/apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3

Repository: git+http://download.alces-software.com/git/packager-base@85035c8
Package: apps/lofreq/0.6.1@18d95c51
Last update: 2013-12-05

Builder: root@headnode1.lampredi.cluster.local
Build date: 2013-12-05T16:00:29
Build modules: apps/python/2.7.3/gcc-4.4.6
Compiler: compilers/gcc/system
System: Linux 2.6.32-279.2.1.el6_lustre.gc46c389.x86_64 x86_64
Arch: Intel(R) Xeon(R) CPU E5620 @ 2.40GHz, 2×4 (b6b89932)
Dependencies: libs/gcc/system (using: libs/gcc/system)
apps/python/2.7.3/gcc-4.4.6 (using: apps/python/2.7.3/gcc-4.4.6)

For further information, execute:

module help apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3

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$ module help apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3

———– Module Specific Help for ‘apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3’ —————————

======== LoFreq ========
fast and sensitive variant-caller for inferring SNVs from
high-throughput sequencing data
=======================

This module sets up your environment for the use of the ‘lofreq’
application. This module sets up version ‘0.6.1’ of the
application.

>> SYNOPSIS << LoFreq is a fast and sensitive variant-caller for inferring single-nucleotide variants (SNVs) from high-throughput sequencing data. It is designed to robustly call low-frequency variants by exploiting base-call quality values. LoFreq has been used to call rare variants in viral and bacterial sequencing datasets and can be used to study mitochondrial heteroplasmy and rare somatic mutations in heterogeneous tumors. LoFreq makes full use of base-call qualities (and versions >=0.5
also use read mapping qualities) which are usually ignored by other
methods or only used for filtering. It is very sensitive; most
notably, it is able to predict variants below the average base-call
quality (i.e. sequencing error rate). Each SNV call is assigned a
p-value which allows for rigorous false positive control. Even
though it uses no approximations or heuristics, it is very efficient
due to several runtime optimizations. LoFreq is generic and fast
enough to be applied to high-coverage data and large genomes. It
takes a minute to analyze Dengue genome sequencing data with nearly
4000X coverage, roughly one hour to call SNVs on a 600X coverage
E.coli genome and 1.5 hours to run on a 100X coverage human exome
dataset.

>> LICENSING << This package is made available subject to the following license(s): BSD License Please refer to the website for further details regarding licensing. >> FURTHER INFORMATION << More information about this software can be found at the website: http://sourceforge.net/p/lofreq/wiki/Home/ For further details regarding this module, including the environment modifications it will apply, execute: module show apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3 >> GET STARTED <<

Please refer to the website for further details on usage of this
package.

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$ module show apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3
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/opt/gridware/etc/modules/apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3:

module-whatis

Repository: git+http://download.alces-software.com/git/packager-base@85035c8
Package: apps/lofreq/0.6.1@18d95c51
Last update: 2013-12-05

For further information, execute:

module help apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3

module-prereq libs/gcc/system
module-prereq apps/python/2.7.3/gcc-4.4.6
module-conflict apps/lofreq
setenv LOFREQDIR /opt/gridware/pkg/apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3
setenv LOFREQBIN /opt/gridware/pkg/apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3/bin
setenv LOFREQPYTHON /opt/gridware/pkg/apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3/python
prepend-path PATH /opt/gridware/pkg/apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3/bin
prepend-path PYTHONPATH /opt/gridware/pkg/apps/lofreq/0.6.1/gcc-4.4.6+python-2.7.3/python/lib/python2.7/site-packages

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Lampredi HPC
igm-lampredi-users@ncl.ac.uk

IGM IT
igmithelp@ncl.ac.uk
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