Minimap2 - Map Reads To Reference

Align reads to the reference genome.

Location

• Filepath: <SnakeLines_dir>/rules/single_end/mapping/mapper/minimap2.snake
• Rule name: minimap2__map_reads_to_reference

Input(s):

• reads: gzipped fastq file with reads, e.g. ‘reads/%s/{sample}.fastq.gz’
• ref: Reference genomic sequences in fasta format

Output(s):

• sam: Ordered mapped reads according to their location on reference genome

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/single_end/mapping/mapper/bowtie2.snake
• Rule name: bowtie2__map_reads_to_reference

Input(s):

• read: gzipped fastq file with reads, e.g. ‘reads/%s/{sample}_R1.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