Short Read Aligners

from http://cdwscience.blogspot.com/

General Purpose Aligners:

• BWA
• Bowtie
• Novoalign
• commercial software covering a variety of alignment needs (RNA-Seq, miRNA-Seq, DNA-Seq, BS-Seq, etc.)
• some functionality is also available in the free version

RNA-Seq Aligners:

• Tophat
• STAR
• very fast aligner

BS-Seq Aligners:

• Bismark
• BSMAP
• BSmooth
• aligner + statistical analysis