Page History

SE:

• bwa aln <R1>
• bwa samse

PE:

• bwa aln <R1>
• bwa aln <R2>
• bwa sampe

• simple to use (take default options)
• good for basic global alignment

• multiple steps needed

• extremely configurable
• can be used for RNAseq alignment because of its many options

• complex (many options)

• simple to use (take default options)
• very fast
• no adapter trimming needed
• good for simple RNAseq analysis
  • the secondary alignments it reports provide splice junction information

• always produces alignments with secondary reads
  • must be filtered if not desired

• extremely configurable
• no adapter trimming needed
• good for small RNA alignment because of its many options

• complex – many options