Bowtie2 - Prepare Index¶
Generate mapping index that is utilized by Bowtie2 algorithm to map reads to a reference genome
Location
- Filepath: <SnakeLines_dir>/rules/shared/mapping/mapper/indices/bowtie2_index.snake
- Rule name: bowtie2__prepare_index
Input(s):
- fa: fasta reference genome
Output(s):
- indecis: 6 files with indeces. e.g ‘{fadir}/bowtie2_index/{sequence}.[1-4].bt2’, ‘{fadir}/bowtie2_index/{sequence}.rev.[1,2].bt2’
Param(s):
- index: name of output reference, technically filename’s path prefix, e.g. ‘{fadir}/bowtie2_index/{sequence}’
Bwa - Prepare Index¶
Generate mapping index that is utilized by BWA algorithm to map reads to a reference genome
Location
- Filepath: <SnakeLines_dir>/rules/shared/mapping/mapper/indices/bwa_index.snake
- Rule name: bwa__prepare_index
Input(s):
- fa: fasta reference genome
Output(s):
- indecis: 5 files with indeces. e.g ‘{fadir}/bwa_index/{sequence}.[amb,ann,bwt,pac,sa]’
Param(s):
- index: output filename’s path prefix, e.g. ‘{fadir}/bwa_index/{sequence}’
Bismark - Prepare Index¶
Generate mapping index that is utilized by Bismark algorithm to map bisulfide treated reads to a reference genome
Location
- Filepath: <SnakeLines_dir>/rules/shared/mapping/mapper/indices/bismark_index.snake
- Rule name: bismark__prepare_index
Input(s):
- fa: fasta reference genome
Output(s):
- ct_index: CT reference index (created by rule bismark__prepare_index)
- ga_index: GA reference index (created by rule bismark__prepare_index)
Param(s):
- fadir: root directory of the reference sequence