Hydra-genetics prealignment module

The prealignment module consists of alignment pre-processing steps, such as trimming and merging of .fastq-files as well as filtering out rRNA sequences from RNA reads. We strongly recommend trimming .fastq-files prior to alignment. For rRNA filtering, SortMeRNA can additionally be used.

Enable trimming

Trimmer software rule must be specified in your config.yaml file. Example:

trimmer_software: "fastp_pe"

Can be set to None for no trimming and only merging.

Enable subsampling

Subsampling of trimmed fastq files can be enabled by specifying subsampling software in your config.yaml file. Example:

subsampling: "seqtk"

Can be set to None or skipped for no subsampling of trimmed reads.

Module input files

Fastq files are the main input data of the prealignment module. These should be specified in units.tsv as well as sequencing meta data. See input data for further information on how to generate these automatically from .fastq files.

Example samples.tsv with all required columns:

sample
sample1

Example units.tsv with all required columns:

sample	type	platform	machine	flowcell	lane	barcode	fastq1	fastq2	adapter
sample1	N	NextSeq	NDX550220	HKTG2BGXG	L001	ACG+ACG	sample1_R1.fastq.gz	sample1_R2.fastq.gz	AGAT,ACAT

Module output files

Trimmed and merged fastq-files are the main output files of the prealignment module.

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