Mercurial > repos > rnateam > segemehl
changeset 1:468b59eae694 draft
Uploaded
| author | bgruening |
|---|---|
| date | Sat, 18 Jan 2014 05:26:31 -0500 |
| parents | 94926c35b6f3 |
| children | dc63d59e7bf8 |
| files | segemehl.xml tool-data/segemehl_indices.loc.sample tool_dependencies.xml |
| diffstat | 3 files changed, 14 insertions(+), 9 deletions(-) [+] |
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--- a/segemehl.xml Thu Oct 17 04:07:29 2013 -0400 +++ b/segemehl.xml Sat Jan 18 05:26:31 2014 -0500 @@ -1,5 +1,5 @@ -<tool id="segemehl" name="segemehl" version="0.1"> - <description>suffix arrays based short read aligner</description> +<tool id="segemehl" name="segemehl" version="0.1.6.0"> + <description>based short read aligner</description> <requirements> <requirement type="package" version="0.1.6">segemehl</requirement> </requirements> @@ -17,7 +17,7 @@ segemehl.x ## number of threads - -t 4 + -t "\${GALAXY_SLOTS:-12}" ## db file path -d ${refGenomeSource.index.fields.db_path} @@ -139,13 +139,19 @@ **What it does** -Segemelt is a short read mapper with gaps. +Segemehl_ is a short read mapper with gaps. -segemehl is a software to map short sequencer reads to reference genomes. +Segemehl_ is a software to map short sequencer reads to reference genomes. Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions. Furthermore, segemehl is not limited to a specific read length and is able to mapprimer- or polyadenylation contaminated reads correctly. -segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, -reads gziped queries to save both disk and memory space and allows bisulfite sequencing mapping and split read mapping. +segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl_ allows bisulfite sequencing mapping and split read mapping. + +.. _Segemehl: http://www.bioinf.uni-leipzig.de/Software/segemehl/ + +**References** + +Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermueller J: "Fast mapping of short sequences with mismatches, insertions and deletions using index structures", PLoS Comput Biol (2009) vol. 5 (9) pp. e1000502 +download latest version: 0.1.6 manual: download here new stuff: faster multiple split read mapping bug fixes: bugfixes: increased sensitivity for strand switches changes: - default accuracy now 90% older segemehl indices are still usable. issues: untraceable errors with gcc compiler gcc-4.5. zlib linker problems with some ubuntu versions complaint department: steve bioinf uni leipzig deshapeimage_1_link_0shapeimage_1_link_1 </help> </tool>
--- a/tool-data/segemehl_indices.loc.sample Thu Oct 17 04:07:29 2013 -0400 +++ b/tool-data/segemehl_indices.loc.sample Sat Jan 18 05:26:31 2014 -0500 @@ -25,6 +25,5 @@ # #hg18canon hg18 hg18 Canonical /data/0/galaxy/segemehl/hg18/chromosomes_can.fa /data/0/galaxy/segemehl/hg18/chromosomes_can.idx #hg18full hg18 hg18 Full /data/0/galaxy/segemehl/hg18/chromosomes_full.fa /data/0/galaxy/segemehl/hg18/chromosomes_full.idx -#/orig/path/hg19 hg19 hg19 /data/0/galaxy/segemehl/hg19/chromosomes.fa /data/0/galaxy/segemehl/hg19/chromosomes.idx #...etc... #
--- a/tool_dependencies.xml Thu Oct 17 04:07:29 2013 -0400 +++ b/tool_dependencies.xml Sat Jan 18 05:26:31 2014 -0500 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="segemehl" version="0.1.6"> - <repository changeset_revision="15c10db35624" name="package_segemehl_0_1_6" owner="rnateam" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="e9455aa5c7e6" name="package_segemehl_0_1_6" owner="rnateam" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>