[Blends-commit] r4013 - /projects/med/trunk/debian-med/tasks/bio

[tille at users.alioth.debian.org]

Author: tille
Date: Wed Apr  9 07:06:50 2014
New Revision: 4013

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=4013
Log:
smalt is now in svn

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=4013&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio	(original)
+++ projects/med/trunk/debian-med/tasks/bio	Wed Apr  9 07:06:50 2014
@@ -562,6 +562,11 @@
  support GNUstep.
 
 Depends: situs
+
+Depends: smalt
+Remark: This can be regarded as successor of ssaha2
+ This program is from the same author as ssaha2 and according to its author
+ faster and more precise than ssaha2 (except for sequences > 2000bp).
 
 Depends: snpeff
 
@@ -2460,31 +2465,6 @@
  at various functional and taxonomic levels applying statistical tests as
  well as hierarchical clustering, multidimensional scaling and heatmaps.
 
-Depends: smalt
-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.
-Remark: This can be regarded as successor of ssaha2
- This program is from the same author as ssaha2 and according to its author
- faster and more precise than ssaha2 (except for sequences > 2000bp).
-
 
 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