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

Here

Guidelines

• Language: C++
• Coding Style: Google C++ Style
• Version Control: git
• Developer Design Document: sometime later...
• User Manual: to be decided, but here are some references
• Testing: a suite once we get something working, the Maq paper gives some insight into the difficulties and solutions of testing alignments.

Research Journals

Daniel's Journal

Jay's Journal

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...

Here

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...

Creating New TWiki Topics

Setting Up a Git Repository

Using Git During Development

Using CMake

Running bowtie, bwa, Mosaik, and SAMTools

Ticgit and You

Using Valgrind

Sharing files and permissions