bowtie2

基本命令

bowtie2-build ref1.fa bowtie2/ref1.fa
bowtie2 -x ref1.fa -U reads_1.fq
bowtie2 -x  bowtie2/ref1.fa -1 reads_1.fq -2 reads_2.fq 

docker run -it  --rm -v $PWD:$PWD -w $PWD  --user 1011:1011 registry.cn-hangzhou.aliyuncs.com/sj-bioinfo/bowtie2:2.5.1  bowtie2-build GRCh38.p14.genome.fa GRCh38.p14.genome.fa 

关键的参数

Presets:

• For --end-to-end:
  • --very-fast -D 5 -R 1 -N 0 -L 22 -i S,0,2.50
  • --fast -D 10 -R 2 -N 0 -L 22 -i S,0,2.50
  • --sensitive -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default)
  • --very-sensitive -D 20 -R 3 -N 0 -L 20 -i S,1,0.50
• For --local:
  • --very-fast-local -D 5 -R 1 -N 0 -L 25 -i S,1,2.00
  • --fast-local -D 10 -R 2 -N 0 -L 22 -i S,1,1.75
  • --sensitive-local -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default)
  • --very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50

Alignment:

• -N： max # mismatches in seed alignment; can be 0 or 1 (0)
• -L： length of seed substrings; must be >3, < 32 (22)
• -i： interval between seed substrings w/r/t read len (S,1,1.15)

Effort:

• -D： give up extending after failed extends in a row (15)
• -R： for reads w/ repetitive seeds, try sets of seeds (2)

• Bowtie 2
  • Bowtie 2 is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes.
  • Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB.
  • Bowtie 2 supports gapped, local, and paired-end alignment modes.