snoStrip - an automatic snoRNA annotation pipeline

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Current release: v2.0

Installation

Instruction for installation and configuration of "snoStrip" on Linux/Unix machines.

REQUIRED PROGRAMS

The snoStrip pipeline utilizes several open source programs for detection and property extraction of putative snoRNAs. Please ensure that the following programs are correctly installed:

1. snoRNA detection:

   • blastall version 2.2.26 or newer
   • infernal version 1.1 or newer

2. property extraction:

   • MUSCLE version 3.7 or newer

   • RNAsubopt version 2.1.9 or newer

   • fastacmd version 2.2.26 or newer

CONFIGURATION OF SNOSTRIP

The configuration file, the snoStrip pipeline, all necessary packages, and additional scripts are located in the folder 'bin'.

Please move into the snoStrip directory and start the configuration script by

cd bin/
./configure.sh

The configure.sh script will search for all necessary programs and additional scripts. Several snoStrip scripts will be adapted to find the path required modules.

Once the configuration process is finished, the snoStrip pipeline should work properly.

Run snoStrip

Plase read the help page of the snoStrip pipeline.

./snoStrip.pl -h