[Blends-commit] r2731 - /projects/med/trunk/debian-med/tasks/bio

[tille at users.alioth.debian.org]

Author: tille
Date: Fri Apr  1 15:31:30 2011
New Revision: 2731

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=2731
Log:
Added SMALT

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

Modified: projects/med/trunk/debian-med/tasks/bio
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio?rev=2731&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Fri Apr  1 15:31:30 2011
@@ -3686,6 +3686,29 @@
  at various functional and taxonomic levels applying statistical tests as
  well as hierarchical clustering, multidimensional scaling and heatmaps. 
 
+Depends: smalt
+License: "shortly" under GPL
+Homepage: http://www.sanger.ac.uk/resources/software/smalt/
+Pkg-Description: align DNA sequencing reads with genomic reference sequences
+ SMALT reads from a range of sequencing platforms, for example Illumina-Solexa,
+ Roche-454 or ABI-Sanger, can be processed including paired-end reads.
+ .
+ The software employs a perfect hash index of short words (< 20
+ nucleotides long), sampled at equidistant steps along the genomic
+ reference sequences.
+ .
+ For each read, potentially matching segments in the reference are
+ identified from seed matches in the index and subsequently aligned with
+ the read using a banded Smith-Waterman algorithm.
+ .
+ The best gapped alignments of each read is reported including a score
+ for the reliability of the best mapping. The user can adjust the
+ trade-off between sensitivity and speed by tuning the length and spacing
+ of the hashed words.
+ .
+ A mode for the detection of split (chimeric) reads is provided.
+ Multi-threaded program execution is supported. 
+
 
 X-Comment: Not sure whether this can be distributed at all - asking
  might not harm because I've got a serious hint that this software