[med-svn] r5408 - trunk/packages/maq/trunk/debian

[Charles Plessy]

Author: plessy
Date: 2010-11-01 10:16:25 +0000 (Mon, 01 Nov 2010)
New Revision: 5408

Modified:
   trunk/packages/maq/trunk/debian/changelog
   trunk/packages/maq/trunk/debian/control
Log:
Developmemt of Maq stopped in 2008. Its successors are BWA and SAMtools.


Modified: trunk/packages/maq/trunk/debian/changelog
===================================================================
--- trunk/packages/maq/trunk/debian/changelog	2010-11-01 03:47:59 UTC (rev 5407)
+++ trunk/packages/maq/trunk/debian/changelog	2010-11-01 10:16:25 UTC (rev 5408)
@@ -1,3 +1,9 @@
+maq (0.7.1-4) UNRELEASED; urgency=low
+
+  * Developmemt of Maq stopped in 2008. Its successors are BWA and SAMtools.
+
+ -- Charles Plessy <plessy at debian.org>  Mon, 01 Nov 2010 19:10:28 +0900
+
 maq (0.7.1-3) unstable; urgency=low
 
   * Distribute scripts that are not installed by upstream’s

Modified: trunk/packages/maq/trunk/debian/control
===================================================================
--- trunk/packages/maq/trunk/debian/control	2010-11-01 03:47:59 UTC (rev 5407)
+++ trunk/packages/maq/trunk/debian/control	2010-11-01 10:16:25 UTC (rev 5408)
@@ -16,34 +16,9 @@
 Depends: ${shlibs:Depends}, ${misc:Depends}
 Description: maps short fixed-length polymorphic DNA sequence reads to reference sequences
  Maq (short for Mapping and Assembly with Quality) builds mapping assemblies
- from short reads generated by the next-generation sequencing machines. It is
+ from short reads generated by the next-generation sequencing machines. It was
  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.)
- .
- This package is likely to be useful for users working with genetics
- or genomic studies in biology who need to assembly DNA sequences from
- fixed-length sequencers.
+ Developmemt of Maq stopped in 2008. Its successors are BWA and SAMtools.