Hydra-genetics alignment module

The alignment module consists of alignment steps, such as alignment against a reference genome and duplicate filtering. The module takes .fastq files as input and outputs .bam files. BWA-mem is used to align short read DNA data while Minimap2 or Pbmm2 can be used to long read DNA data. For RNA short read data STAR is used as aligner. Picard is used for duplicate marking and samtools for merging, sorting, and indexing .bam files. When UMI barcodes are used consensus reads are created using fgbio in combination with BWA-mem.

DNA short read steps

DNA long read steps

RNA steps

Module input files for short read data

Trimmed or untrimmed merged .fastq files.

• prealignment/merged/{sample}_{type}_{read}.fastq.gz

Module input files for long read data

Unmapped .bam files specified in the units.tsv under the bam column.

Module output files

Aligned, merged and sorted .bam files as well as chromosome split .bam files for speeding up downstream analysis. UMI-consensus-files get a umi tag added to the bam-filename.

• alignment/samtools_merge_bam/{sample}_{type}.bam
• alignment/picard_mark_duplicates/{sample}_{type}_{chr}.bam
• alignment/bwa_mem_realign_consensus_reads/{sample}_{type}_{chr}.umi.bam
• alignment/samtools_extract_reads_umi/{sample}_{type}_{chr}.umi.bam
• alignment/star/{sample}_{type}.bam
• alignment/star/{sample}_{type}.SJ.out.tab
• alignment/minimap2_align/{sample}_{type}.bam
• alignment/pbmm2_align/{sample}_{type}.bam