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alignment typealigner optionspro'scon's
global with bwa 

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
global with bowtie2bowtie2 --global
  • extremely configurable
  • can be used for RNAseq alignment because of its many options
  • complex (many options)
local with bwa bwa mem
  • 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
local with bowtie2bowtie2 --local
  • extremely configurable
  • no adapter trimming needed
  • good for small RNA alignment because of its many options
  • complex – many options

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