NGSAlignerProject < BETA

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---+ Main page for NGS aligner project

---++ Quick facts

   * *project directory*: =/ubc/cs/research/condon/share/projects/ngs-aligner=
   * *blessed code repository*: =/ubc/cs/research/condon/share/projects/ngs-aligner/src/ngsa_suite.git=

---++ Meetings

   * *bi-weekly supervisor meeting*: =every second Tuesday at 13:45, starting February 2nd, 2010=

---++ Specifications

---++++[[https://bugs.cs.ubc.ca/cgi-bin/twiki/view/BETA/NGSAlignerToDo][Here]]

---++ Guidelines

   * *Language*: C++
   * *Coding Style*: [[http://google-styleguide.googlecode.com/svn/trunk/cppguide.xml][Google C++ Style]]
   * *Version Control*: [[http://git-scm.com/][git]]
   * *Developer Design Document*: sometime later...
   * *User Manual*: to be decided, but [[http://bioinformatics.bc.edu/marthlab/Mosaik#Current_Documentation][here]] [[http://bio-bwa.sourceforge.net/bwa.shtml][are]] [[http://maq.sourceforge.net/maq-man.shtml][some]] [[http://bowtie-bio.sourceforge.net/manual.shtml][references]]
   * *Testing*: a suite once we get something working, the [[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577856/][Maq]] paper gives some insight into the difficulties and solutions of testing alignments.

---++ Research Journals

---++++[[https://bugs.cs.ubc.ca/cgi-bin/twiki/view/BETA/DanielsJournal][Daniel's Journal]]
---++++[[https://bugs.cs.ubc.ca/cgi-bin/twiki/view/BETA/JaysJournal][Jay's Journal]]
---++++[[https://bugs.cs.ubc.ca/cgi-bin/twiki/view/BETA/JaysTermTwoJournal][Jay's Journal (Term 2)]]

---++ Discussion

Random thoughts that would benefit from others' input, that are either too trivial too spam in email, or somewhat complex that would generate a rather gruesome email chain...

---++++[[https://bugs.cs.ubc.ca/cgi-bin/twiki/view/BETA/NGSAlignerDiscussion][Here]]

---++++[[https://bugs.cs.ubc.ca/cgi-bin/twiki/view/BETA/CurrentSpeeds][Current speed comparisons]]
---++ Short Guides

I should disclaim that I haven't actually tested these... so I wouldn't be surprised to find some errors somewhere...

[[https://bugs.cs.ubc.ca/cgi-bin/twiki/view/BETA/WikiTopicCreation][Creating New TWiki Topics]]

[[https://bugs.cs.ubc.ca/cgi-bin/twiki/view/BETA/SettingUpGitRepo][Setting Up a Git Repository]]

[[https://bugs.cs.ubc.ca/cgi-bin/twiki/view/BETA/GitWorkFlow][Using Git During Development]]

[[https://bugs.cs.ubc.ca/cgi-bin/twiki/view/BETA/CMakeUsage][Using CMake]]

[[https://bugs.cs.ubc.ca/cgi-bin/twiki/view/BETA/RunningAligners][Running bowtie, bwa, Mosaik, and SAMTools]]

[[https://bugs.cs.ubc.ca/cgi-bin/twiki/view/BETA/TicGitUsage][Ticgit and You]]

[[https://bugs.cs.ubc.ca/cgi-bin/twiki/view/BETA/UsingValgrind][Using Valgrind]]

[[https://bugs.cs.ubc.ca/cgi-bin/twiki/view/BETA/FixingPermissions][Sharing files and permissions]]
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Topic revision: r107 - 2011-01-05 - jayzhang