Links
Useful books/talks/tutorials
Programming/Analysis
Linux/shell
Absolute basics
UNIX Tutorial for Beginners (Michael Stonebank)
Learning the Shell (William Shotts)
Intermediate, Shell Programming
Introduction to Linux: A Hands on Guide (Machtelt Garrels)
Linux Shell Scripting Tutorial — A Beginner’s handbook
References/Cheat Sheet
All the Best Linux Cheat Sheets
Linux BASH command line MAN page
Database/SQL
Comparison of different SQL implementations
A nice comparison of the different syntax, behavior of the SQL commands in different platforms.
Python
Programming for Everybody (Getting Started with Python) (Coursera)
Perl
Comprehensive Perl Archive Network (CPAN)
R
The Comprehensive R Archive Network (CRAN)
Scientific Writing and Presentation
The Craft of Scientific Presentations: Critical Steps to Succeed and Critical Errors to Avoid
The Elements of Style (William Strunk, Jr.)
Scientific Writing and Communication: Papers, Proposals, and Presentations
Online resources
NIH traning series, many good presentations about career development and general matters in academics.
Complied by Joe Felsenstein at UW. A very comprehensive collection for online phylogeny analysis program/packages.
Broad/Illumina Genome Analyzer Boot Camp
An online course for all the basic information you should know (and more) for Illumina sequencing.