OLego Documentation v1.0.6

What is OLego?

OLego is a program specifically designed for de novo spliced mapping of mRNA-seq reads. OLego adopts a seed-and-extend scheme, and does not rely on a separate external mapper. It achieves high sensitivity of junction detection by strategic searches with very small seeds (12-14 nt), efficiently mapped using Burrows-Wheeler transform (BWT) and FM-index. This also makes it particularly sensitive for discovering small exons. It is implemented in C++ with full support of multiple threading, to allow for fast processing of large-scale data.

OLego is an open source code project and released under GPLv3. The implementation of OLego relies heavily on BWA (version 0.5.9rc1, http://bio-bwa.sourceforge.net/). It also uses some source code from the Jim Kent source code tree (http://genome.ucsc.edu/admin/git.html).

Versions

• v1.0.6 ( 08-09-2012 )
  • Added option –max-multi (default:1000) to avoid huge data in a single line.
  • Added option –num-reads-batch.
  • Fixed a bug in the junction connecting step.
• v1.0.5 ( 07-16-2012 )
  • Minor bug fixed (the old code crashes in a very rare case).
  • v1.0.4 ( 06-12-2012 )
  • Option changes ( do single-anchor search by default now ).
• v1.0.3 ( 06-10-2012 )
  • Now supports strand specific library
  • Fixed bugs about XS
• v1.0.0 ( 05-15-2012 )
  • The initial Public release

Prerequisites

The major programs of OLego ( olego and olegoindex ) can be installed and ran on Unix-based system (Linux or MacOS) with GCC compiler installed. We provided scripts for post analysis and regression model construction, these codes may require Perl and R.

Download

The code and binary files can be found at http://sourceforge.net/projects/ngs-olego/files/ , we are regularly updating the code, so please check regularly to keep your code updated. The code can also be reached via git:

git clone git://git.code.sf.net/p/ngs-olego/code ngs-olego-code

The main programs of OLego (olego and olegoindex ) can be installed and run on Unix-based system with GCC compiler installed. We also provide scripts for post analysis and regression model construction. These codes may require Perl and R installed.

Installation

To compile OLego on your computer, please go to the OLego directory and type:

make

If everything goes right, you will find two executable files olegoindex and olego in the folder.

We also provide binary executable files at http://sourceforge.net/projects/ngs-olego/files/ for x86_64 and i686 Linux systems.

Please feel free to report any problems you come up with.

Usage

Build the index for the genome sequence

To run OLego, you need a BWT index for the reference sequences. We use exactly the same genome index used by BWA. For your convience, you can build the index with olegoindex that comes with this package:

olegoindex [-a bwtsw|div|is] [-p STR] <in.fasta>

Arguments:

Argument	Description
<in.fasta>	This is the fasta format file with the reference sequence. Please put all the sequences (from different chromosomes ) in a single file.

Options:

Option	Description
-a	BWT construction algorithm: bwtsw or is [default: bwtsw]
-p	prefix of the index [default: the same as the fasta file name]

Caution: please use “-a bwtsw” for long genome (like human or mouse genome).

There will be 8 files (prefix.pac, prefix.ann, prefix.amb, prefix.rpac, prefix.bwt, prefix.rbwt, prefix.sa, prefix.rsa ) generated after olegoindex finishes.