InteMAP

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Description

InteMAP (Integrated Metagenomic Assembly Pipeline) is a pipeline which integrates individual assemblers for assembling metagenomic short sequencing reads. By integrating three assemblers IDBA_UD, ABySS, and CABOG, InteMAP takes advantage of their strengths on assembling species with special sequencing coverage depths, and generates a high quality assembly.InteMAPis suitable for unix-like system with gcc and python installed.

Usage

Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules

to your script before loading a module. Then, you can list all versions of intemap and load default version of intemap as

module avail intemap/ # list available modules
module load intemap   # load (default) module


If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail intemap

and choose explicit version you want to use.

Documentation

http://cqb.pku.edu.cn/ZhuLab/InteMAP/Manual.pdf

Homepage

http://cqb.pku.edu.cn/ZhuLab/InteMAP/index.html