This document discusses next generation sequencing methods like 454 sequencing, Illumina sequencing, and SOLiD sequencing. It then describes how the large amounts of sequencing data generated can be used for transcriptome analysis to study gene expression, identify new genes, and analyze non-model organisms. Finally, it outlines some of the common bioinformatics tools used for assembling sequencing reads, detecting SNPs, finding homologous genes, identifying open reading frames, and annotating genes.