[Cdd-commits] r945 - projects/med/trunk/debian-med/tasks

[CDD Subversion Commit]

Author: tille
Date: Tue Jul  8 12:33:37 2008
New Revision: 945

Modified:
   projects/med/trunk/debian-med/tasks/bio
Log:
Added maq; changed name of beast (there is just a package with this name)


Modified: projects/med/trunk/debian-med/tasks/bio
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Tue Jul  8 12:33:37 2008
@@ -1579,7 +1579,7 @@
  extensions to tRNAscan-SE detect unusual tRNA homologues such as selenocysteine
  tRNAs, tRNA-derived repetitive elements and tRNA pseudogenes.
 
-Depends: beast
+Depends: beast-mcmc
 Homepage: http://beast.bio.ed.ac.uk/
 License: LGPL
 Pkg-Description: Bayesian MCMC analysis of molecular sequences
@@ -1593,6 +1593,9 @@
  setting up standard analyses and a suit of programs for analysing the results.
  .
  The source is avialable at http://code.google.com/p/beast-mcmc/ .
+ .
+ Please note: There is a Debian package beast which is completely unrelated
+ to this project.
 
 Depends: artemis
 Homepage: http://www.sanger.ac.uk/Software/Artemis/
@@ -1604,3 +1607,37 @@
  available for UNIX, Macintosh and Windows systems. It can read EMBL and GENBANK
  database entries or sequence in FASTA or raw format. Extra sequence features
  can be in EMBL, GENBANK or GFF format.
+
+Depends: maq
+Homepage: http://maq.sourceforge.net/
+License: GPL
+Pkg-URL: http://svn.debian.org/wsvn/debian-med/trunk/packages/maq/trunk/?rev=0&sc=0
+Pkg-Description: Mapping and Assembly with Quality
+ Maq builds mapping assemblies from short reads generated by the
+ next-generation sequencing machines. It is particularly designed for
+ Illumina-Solexa 1G Genetic Analyzer, and has a preliminary functionality to
+ handle ABI SOLiD data. Maq is previously known as mapass2.
+ .
+ With Maq you can:
+  - Fast align Illumina/SOLiD reads to the reference genome. With the
+    default options, one million pairs of reads can be mapped to the
+    human genome in about 10 CPU hours with less than 1G memory.
+  - Accurately measure the error probability of the alignment of each
+    individual read.
+  - Call the consensus genotypes, including homozygous and heterozygous
+    polymorphisms, with a Phred probabilistic quality assigned to each base.
+  - Find short indels with paired end reads.
+  - Accurately find large scale genomic deletions and translocations with
+    paired end reads.
+  - Discover potential CNVs by checking read depth.
+  - Evaluate the accuracy of raw base qualities from sequencers and help
+    to check the systematic errors.
+ .
+ However, Maq can NOT:
+  - Do de novo assembly. (Maq can only call the consensus by mapping reads
+    to a known reference.)
+  - Map shorts reads against themselves. (Maq can only find complete overlap
+    between reads.)
+  - Align capillary reads or 454 reads to the reference. (Maq cannot align
+    reads longer than 63bp.)
+