Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv14630
Added Files:
lofreq.info
Log Message:
new pkg lofreq 0.6.0
--- NEW FILE: lofreq.info ---
Package: lofreq
Version: 0.6.0
Revision: 1
Description: Fast and sensitive variant-caller
License: GPL
Maintainer: Hanspeter Niederstrasser <nie...@users.sourceforge.net>
Depends: <<
python27,
python27-shlibs
<<
BuildDepends: <<
python27
<<
Source: mirror:sourceforge:%n/%v/%n-%v.tar.gz
Source-MD5: a15acb315ca2b79459ad2338ba14018f
PatchScript: <<
### The python installer bit doesn't take DESTDIR
perl -pi -e 's|prefix '\''\$\(prefix\)'\''|$& --root %d|g'
src/lofreq_python/Makefile.in
<<
CompileScript: <<
#!/bin/sh -ev
export PYTHON=%p/bin/python2.7
%{default_script}
<<
InstallScript: <<
#!/bin/sh -ev
make -w install DESTDIR=%d
<<
DocFiles: AUTHORS COPYING ChangeLog NEWS README
Homepage: http://sourceforge.net/p/lofreq/
DescDetail: <<
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.
For more details see:
Andreas Wilm, Pauline Poh Kim Aw, Denis Bertrand, Grace Hui Ting Yeo,
Swee Hoe Ong, Chang Hua Wong, Chiea Chuen Khor, Rosemary Petric, Martin
Lloyd Hibberd and Niranjan Nagarajan. LoFreq: A sequence-quality aware,
ultra-sensitive variant caller for uncovering cell-population heterogeneity
from high-throughput sequencing datasets. Nucleic Acids Res. 2012;
40(22):11189-201.
<<
DescUsage: <<
All script-names start with lofreq_ and print a simple help message
when invoked with -h.
<<
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