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author Petar Petrov2016-06-05 14:52:22 +0200
committer Willy Sudiarto Raharjo2016-06-05 17:28:04 +0200
commita2d9c58b502099a081d58b0664334fa44b8bde2f (patch)
tree1098fd3502ae47e577eae4ef78bc3df06feeec1b /academic/ugene/README
parentb6456152b10e4c01ee304557130dc8b19747186a (diff)
downloadslackbuilds-a2d9c58b502099a081d58b0664334fa44b8bde2f.tar.gz
academic/ugene: Updated for version 1.22.0
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
Diffstat (limited to 'academic/ugene/README')
-rw-r--r--academic/ugene/README18
1 files changed, 11 insertions, 7 deletions
diff --git a/academic/ugene/README b/academic/ugene/README
index a163595629..5ed2a5eaa6 100644
--- a/academic/ugene/README
+++ b/academic/ugene/README
@@ -21,19 +21,28 @@ be launched on local resources or in a High Performance Computing
built-in plugin system and structured UGENE API make it possible to
extend the toolkit with new functionality.
+CITING:
+Unipro UGENE: a unified bioinformatics toolkit
+Konstantin Okonechnikov; Olga Golosova; Mikhail Fursov; the UGENE team
+Bioinformatics 2012 28: 1166-1167
+
EXTERNAL TOOLS
UGENE can use and drive a number of external tools, providing a nice
and unified GUI. These are not needed at build time, but are highly
recommended for the complete (and extended) functionality of the
-program. Almost all of them can be found at SlackBuilds.org:
+program. All of them are available at SlackBuilds.org:
+- bedGraphToBigWig (Convert bedGraph to bigWig file)
- bedtools (A powerful toolset for genome arithmetic)
- bowtie (A short read aligner of DNA sequences)
- bowtie2 (A tool for aligning sequencing reads)
- bwa (Burrows-Wheeler Aligner)
- cap3 (CAP3: A DNA sequence assembly program)
- cistrome-CEAS (CEAS: Cis-regulatory Element Annotation System)
+- cistrome-conductGO (Find the top-n highest expressed TFs)
+- cistrome-extra (Cistrome Applications Harvard extra apps)
- cistrome-MACS (MACS: Model-based Analysis of ChIP-Seq)
+- cistrome-mdseqpos (Cistrome Applications Harvard mdseqpos)
- clustalo (Clustal Omega)
- clustalw (Multiple Sequence Alignment)
- cufflinks (A reference-guided assembler for RNA-Seq experiments)
@@ -52,9 +61,4 @@ program. Almost all of them can be found at SlackBuilds.org:
- vcftools (A program package designed for working with VCF files)
Alternatively, check the program's website if you want to get them
-precompiled.
-
-CITING:
-Unipro UGENE: a unified bioinformatics toolkit
-Konstantin Okonechnikov; Olga Golosova; Mikhail Fursov; the UGENE team
-Bioinformatics 2012 28: 1166-1167
+precompiled: http://ugene.net/external.html