Sequence Imp Readme (Part of the Kraken framework).

A broader explanation of the pipeline Sequence Imp can be found in the online
documentation (http://www.ebi.ac.uk/research/enright/software/kraken), a copy 
of which can be found in the doc/ directory. This provides a full description
of the files and information that you will need to analyse small RNA sequencing
data with the pipeline.

In order to get started first of all you should read the "Additional software
dependencies" section of the manual. This will help you set
up the pipeline and direct you to the additional tools and libraries required.
To test your system setup once these are installed, either run the
runmefirst.sh script or initiate imp_commandline.pl --system-setup. This should
identify any resources you are still missing.

Initially you may find it advantageous to run through some example data. 
This is described in detail on the Kraken website
(http://www.ebi.ac.uk/research/enright/software/kraken). 

imp_commandline.pl --help will give you a summary of the options available to a
user with which to control the pipeline. It also provides a brief introduction
on how to get started.

This software is covered by the GPL v3 software license. For more information
please see LICENSE.

Good luck and please contact us at kraken@ebi.ac.uk with any feedback or
problems that you might have.