Bwa - Map Reads To Reference

For input preprocessed reads bwa finds the most similar genomic region in the provided reference genome, using bwa mem algorithm.

Location

  • Filepath: <SnakeLines_dir>/rules/paired_end/mapping/mapper/bwa.snake
  • Rule name: bwa__map_reads_to_reference

Input(s):

  • r1: gzipped fastq file with left reads, e.g. ‘reads/%s/{sample}_R1.fastq.gz’
  • r2: gzipped fastq file with right reads, e.g. ‘reads/%s/{sample}_R2.fastq.gz’
  • index: reference index (created by rule bwa__prepare_index), e.g. ‘reference/{reference}/bwa_index/{reference}.bwt’

Output(s):

  • bam: mapped read in BAM file, e.g. ‘mapping/{reference}/original/{sample}.bam’

Param(s):

  • index: name of reference, technically filename’s path prefix, e.g. ‘reference/{reference}/bwa_index/{reference}’
  • additional: additional params
  • concordant: more strict conditions for scoring options should help to map only concordant reads

Bismark - Map Methyl Seq Reads To Reference

For input preprocessed reads treated by Bisulfide Bismark finds the most similar genomic region in the provided reference genome.

Location

  • Filepath: <SnakeLines_dir>/rules/paired_end/mapping/mapper/bismark.snake
  • Rule name: bismark__map_methyl_seq_reads_to_reference

Input(s):

  • r1: gzipped fastq file with left reads, e.g. ‘reads/%s/{sample}_R1.fastq.gz’
  • r2: gzipped fastq file with right reads, e.g. ‘reads/%s/{sample}_R2.fastq.gz’
  • ct_index: CT reference index (created by rule bismark__prepare_index)
  • ga_index: GA reference index (created by rule bismark__prepare_index)
  • ref: reference genome, i.e. ‘reference/{reference}/{reference}.fa’

Output(s):

  • bam: mapped reads in BAM format
  • alignment_report: Control report with basic mapping statistics generated by Bismark

Param(s):

  • aux_bam: bam file that have preset name by Bismark. Has to be renamed to match downstream analysis.
  • aux_alignment_report: alignment report that have preset name by Bismark. Better to move to separate folder to keep bam directory clean
  • bam_dir: directory with the output bam file
  • reference_dir: directory with reference fasta, i.e. ‘reference/{reference}’

Bowtie2 - Map Reads To Reference

For input preprocessed reads bowtie2 finds the most similar genomic region in the provided reference genome.

Location

  • Filepath: <SnakeLines_dir>/rules/paired_end/mapping/mapper/bowtie2.snake
  • Rule name: bowtie2__map_reads_to_reference

Input(s):

  • r1: gzipped fastq file with left reads, e.g. ‘reads/%s/{sample}_R1.fastq.gz’
  • r2: gzipped fastq file with right reads, e.g. ‘reads/%s/{sample}_R2.fastq.gz’
  • index: reference index (created by rule bowtie2__prepare_index), e.g. ‘reference/{reference}/bowtie2_index/{reference}.1.bt2’
  • ref: reference genome, e.g. ‘reference/{reference}/{reference}.fa’

Output(s):

  • bam: mapped read in BAM file, e.g. ‘mapping/{reference}/original/{sample}.bam’

Param(s):

  • index: name of reference, technically filename’s path prefix, e.g. ‘reference/{reference}/bowtie2_index/{reference}’
  • additional: additional params
  • concordant: only concordant reads