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

UNIX/LINUX Reference Card

Linux Quick Reference Linux (O'Reilly)

Linux BASH command line MAN page

Database/SQL

Beginning SQL by Paul Wilton, John Colby

It's an OK beginner book, there are nice examples throughout the book (lots of printout codes and results).

MySQL 5.5 Reference Manual

Oracle 11g documentation

Comparison of different SQL implementations

A nice comparison of the different syntax, behavior of the SQL commands in different platforms.

Python

Python Programming for the absolute beginner

Byte_of_Python (for Python 3)

Dive into Python: Python from novice to pro

Perl

Comprehensive Perl Archive Network (CPAN)

Learning Perl, 3rd Edition

Beginning Perl for Bioinformatics

R

The Comprehensive R Archive Network (CRAN)

CRAN Manuals

Simple R

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

Scientific Writing Booklet (Marc Tischler, Univ of Arizona)

Online resources


NIH Training&Education Series

NIH traning series, many good presentations about career development and general matters in academics.

Phylogeny programs

Complied by Joe Felsenstein at UW. A very comprehensive collection for online phylogeny analysis program/packages.

An Alphabetic List of Genetic Analysis Software

A very comprehensive collection for online phylogeny analysis program/packages. It's brief history can be found on their website.

NGS and microarray software

A free informative directory for next-generation sequencing (NGS) and microarray data analysis.

Broad/Illumina Genome Analyzer Boot Camp

An online course for all the basic information you should know (and more) for Illumina seuqencing.