NGSANE is a framework for advanced production informatics of Next Generation Sequencing libraries.

Version: v0.5.2.0

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Associated publication

"NGSANE: A Lightweight Production Informatics Framework for High Throughput Data Analysis" Buske FA, French HJ, Smith MA, Clark SJ, Bauer DC Bioinformatics 2014 May 15;30(10):1471-2. doi: 10.1093/bioinformatics/btu036. Epub 2014 Jan 26.

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Setup:

Define the environment variable NGSANE_BASE and point it to the directory that contains the NGSANE framework. You may want to set up $NGSANE_BASE environment variable on the cluster or in your .bash_rc or .profile You can also specify it in the project-based config file.

For more information check out the wiki at https://github.com/BauerLab/ngsane/wiki

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Structure of NGSANE:

ngsane

bin/ contains the trigger.sh script that is used to launch any and all jobs by supplying an appropriate config file
conf/ contains the config file for the cluster environment at hand. Rename the sample_header.sh template into header.sh and populate the variables contained within with the values specific to your system
core/ contains the core scripts handling job submission, logging and report generation etc.
doc/ contains documents/presentations/publication describing the framework
mods/ contains all modules currently available from within NGSANE
sampleConfigs/ contains a sample config file for various pipelines/modules than can be triggered in the NGSANE framework copy the corresponding file(s) to your data and customise as appropriate
tools/ contains various helper scripts used within the modules, mostly tapping into Python and R

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How to create a new project:

NGSANE requires a config file for each of your projects and a (set of) fastq files that need to be placed in a simple but predefined structure.

Make a new folder for your project and create the following folder structure:

- fastq - - - - - .fastq[.gz] - - - .fastq[.gz] (if paired library) - - - .fastq[.gz] - - - .fastq[.gz] (if paired library) - config.txt Here is your project name. The fastq folder contains all raw data grouped by EXPERIMENT (or any other meaningful way). Each EXPERIMENT folder can contain multiple sequencing libraries. You probably want them gzipped to save space. You can add additional EXPERIMENT folders if you like. However, all libraries should have the same ending as well as the same read-pair identification (e.g. have the suffix _R1.fastq.gz for read1 of a zipped fastq). for examples of config files for different pipelines look in the ngsane/sampleConfigs/. ################################################################################ # How to run NGSANE jobs: The main access point is trigger.sh, which can be invoked to run in different modes >trigger.sh options for TASK: [empty] start a dry-run: create folders,prints what will be done new detect new data that has not been processed yet. fetchdata get data from remote server (via smbclient) pushresult puts results to remote server (via smbclient) armed submit tasks to the queue direct run task directly (e.g. on node after qrsh) postonly run only the post analysis steps of a task (if available) verify check the pbs logfiles for errors recover pick up unfinished business (interrupted jobs) html check the pbs logfiles for errors and and make summary HTML page report alias for html trackhubs generate trackhubs clean removes all dummy files Following the folder structure example from above, you can submit jobs using a properly configured config.txt form within the PROJECT folder as follows: PROJECT>trigger.sh ./config.txt armed ################################################################################ Contact: Denis.Bauer - at - csiro.au f.buske - at - garvan.org.au

BauerLab / ngsane

readme

Associated publication

Setup:

Structure of NGSANE:

How to create a new project: