The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability

The NGS wiki book http://en.wikibooks.org/wiki/Next_Generation_Sequencing_(NGS)

http://intl-bib.oxfordjournals.org/content/early/2013/06/21/bib.bbt045.full

for more details, refer to the link above.
Nine simple rules to begin with NGS analysis

RULE 1: DO NOT FEAR THE COMMAND LINE

RULE 2: KNOW THE CONVENTIONS

RULE 3: READ INTRODUCTORY REVIEWS

RULE 4: START WITH QUALITY CHECKING

RULE 5: PLAN FOR MISTAKES AND DOCUMENT WORKFLOW

RULE 6: ALWAYS GET INFORMED AND GET HELP IF STUCK

RULE 7: USE AN EFFICIENT INTEGRATIVE APPROACH

RULE 8: AVOID REINVENTING THE WHEEL  ( I mentioned this several times in my blog :) )

RULE 9: EDUCATION IS IMPORTANT