BOWTIE2 alignment settings

• DEFAULT
  • command:
  • flags: end to end alignment
  • output:
• SENSITIVE
  • command: bowtie2 -a -p 20 -x ORF_with_pDONR --local --very-sensitive-local -U %s -S %s
  • flags: -a: no upper limit of alignment -p 20: 20 thread --local: local alignment --very-sensitive-local
    • -D 20 -R 3 -N 0 -L 20 -i S,1,0.50: zero mismaches,