details: http://www.bx.psu.edu/hg/galaxy/rev/c8ba2a78e696 changeset: 2851:c8ba2a78e696 user: Anton Nekrutenko <anton@bx.psu.edu> date: Thu Oct 08 13:33:54 2009 -0400 description: More interface updates 2 file(s) affected in this change: tools/sr_mapping/bowtie_wrapper.xml tools/sr_mapping/bwa_wrapper.xml diffs (46 lines): diff -r d146ca99434f -r c8ba2a78e696 tools/sr_mapping/bowtie_wrapper.xml --- a/tools/sr_mapping/bowtie_wrapper.xml Thu Oct 08 11:33:43 2009 -0400 +++ b/tools/sr_mapping/bowtie_wrapper.xml Thu Oct 08 13:33:54 2009 -0400 @@ -426,9 +426,19 @@ **What it does** -Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. Reads can be as long as 1024 base pairs, though shorter is better. Bowtie produces a specific output format which is converted to SAM by this tool. +Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml + +------ + +**Know what you are doing** + +.. class:: warningmark + +There is no such thing (yet) as automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading `documentation`__ and experimenting. Fortunaly, Galaxy makes experimenting easy. + + .. __: http://bowtie-bio.sourceforge.net/index.shtml ------ diff -r d146ca99434f -r c8ba2a78e696 tools/sr_mapping/bwa_wrapper.xml --- a/tools/sr_mapping/bwa_wrapper.xml Thu Oct 08 11:33:43 2009 -0400 +++ b/tools/sr_mapping/bwa_wrapper.xml Thu Oct 08 13:33:54 2009 -0400 @@ -291,7 +291,17 @@ **What it does** -**BWA** is a high performance sequence aligner that succeeds MAQ. It is based on BWT-SW but uses a completely different algorithm and is aimed towards short read alignments. It is fast--it can map the human genome in only 15-25 minutes. Heng Li of the Sanger Institute wrote the majority of the code, with contributions by Chi-Kwong Wong at the University of Hong Kong, Nong Ge at Sun Yat-Sen University, and Yuta Mori. +BWA is a fast light-weighted tool that aligns relatively short sequences (queries) to a sequence database (large), such as the human reference genome. It is developed by Heng Li at the Sanger Insitute. + +------ + +**Know what you are doing** + +.. class:: warningmark + +There is no such thing (yet) as automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading `documentation`__ and experimenting. Fortunaly, Galaxy makes experimenting easy. + + .. __: http://bio-bwa.sourceforge.net/ ------