Sequence Alignment Programs

Presentation by Angela Garibaldi

Presentation

Our presentation will include a brief introduction to alignments followed by an interactive tutorial for STAR alignment of the griffith data.

• Slides: RNA-seq Alignments
• Doc: Alignment with STAR

Helpful Resources

Sequence alignment programs:

• STAR
  • paper: "STAR: ultrafast universal RNA-seq aligner"
  • manual
• HISAT2
  • paper: "HISAT: a fast spliced aligner with low memory requirements"
  • manual
• Bowtie2
  • paper: "Fast gapped-read alignment with Bowtie 2"
  • manual

Corresponding Chapters in The BioStar Handbook:

• Chapter 11: Sequence Alignments
• Chapter 13: Short Read Aligners