[Blends-commit] r2635 - /projects/med/trunk/debian-med/tasks/bio-ngs

[tille at users.alioth.debian.org]

Author: tille
Date: Sat Jan 29 15:48:54 2011
New Revision: 2635

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=2635
Log:
Addede more information for prospective packages

Modified:
    projects/med/trunk/debian-med/tasks/bio-ngs

Modified: projects/med/trunk/debian-med/tasks/bio-ngs
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio-ngs?rev=2635&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio-ngs (original)
+++ projects/med/trunk/debian-med/tasks/bio-ngs Sat Jan 29 15:48:54 2011
@@ -3,7 +3,6 @@
  It aims at gettting packages which specializes in alignment of sequences produced by next generation sequencing.
 
 
-X-Begin-Category: High throughput sequencing
 Depends:
 	bwa,
 	last-align,
@@ -12,10 +11,7 @@
 	r-bioc-hilbertvis,
 	samtools,
 	ssake,
-	velvet,
-	saha2,
-	mosaik
-X-End-Category: High throughput sequencing
+	velvet
 
 Depends: bowtie
 Homepage: http://bowtie-bio.sourceforge.net/
@@ -55,3 +51,35 @@
 Published-doi: 10.1101/gr.1917404
 Published-URL: http://pubmed.org/15140833
 
+
+Depends: ssaha2
+Homepage: http://www.sanger.ac.uk/resources/software/ssaha2/
+License: to be clarified
+Pkg-Description: pairwise sequence alignment program
+ SSAHA2 (Sequence Search and Alignment by Hashing Algorithm) is a
+ pairwise sequence alignment program designed for the efficient
+ mapping of sequencing reads onto genomic reference sequences.  SSAHA2
+ reads of most sequencing platforms (ABI-Sanger, Roche 454,
+ Illumina-Solexa) and a range of output formats (SAM, CIGAR, PSL etc.)
+ are supported. A pile-up pipeline for analysis and genotype calling
+ is available as a separate package.
+Published-Title: SSAHA: a fast search method for large DNA databases.
+Published-Authors: Ning Z, Cox AJ and Mullikin JC
+Published-In: Genome research 2001;11;10;1725-9
+Published-doi: DOI: 10.1101/gr.194201
+
+Depends: mosaik-aligner
+Homepage: http://code.google.com/p/mosaik-aligner/
+License: GPL
+Pkg-Description: refrence guided aligner for next-generation sequencing
+ MosaikBuild converts various sequence formats into Mosaik’s native
+ read format. MosaikAligner pairwise aligns each read to a specified
+ series of reference sequences. MosaikSort resolves paired-end reads
+ and sorts the alignments by the reference sequence
+ coordinates. Finally, MosaikText converts alignments to different
+ text-based formats.
+ .
+ At this time, the workflow consists of supplying sequences in FASTA,
+ FASTQ, Illumina Bustard & Gerald, or SRF file formats and producing
+ results in the BLAT axt, the BAM/SAM, the UCSC Genome Browser bed, or
+ the Illumina ELAND formats.