https://hydra-genetics-prealignment.readthedocs.io

hydra-genetics/prealignment

Snakemake module containing processing steps that should be performed before sequence alignment

Visit for more detailed information.

💬 Introduction

The 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. To enable trimming the trimmer_software-stanza in the config.yaml may be set to the name of the trimming rule, e.g. fastp_pe, or None if trimming should be omitted. For rRNA filtering, SortMeRNA can be used. Input data should be specified via samples.tsv and units.tsv.

❗ Dependencies

In order to use this module, the following dependencies are required:

Note! Releases of prealignment <= v0.4.0 needs tabulate<0.9.0 added in requirements.txt

🎒 Preparations

Sample and unit data

Input data should be added to samples.tsv and units.tsv. The following information need to be added to these files:

Column Id	Description
samples.tsv
sample	unique sample/patient id, one per row
units.tsv
sample	same sample/patient id as in samples.tsv
type	data type identifier (one letter), can be one of Tumor, Normal, RNA
platform	type of sequencing platform, e.g. NovaSeq
machine	specific machine id, e.g. NovaSeq instruments have @Axxxxx
flowcell	identifier of flowcell used
lane	flowcell lane number
barcode	sequence library barcode/index, connect forward and reverse indices by +, e.g. ATGC+ATGC
fastq1/2	absolute path to forward and reverse reads
adapter	adapter sequences to be trimmed, separated by comma

Reference data

An array of reference .fasta-files should be specified in config.yaml in the section sortmerna and fasta. These files are readily available as part of the github repo. In addition, these files should be indexed using SortMeRNA and the filepath set at sortmerna and index.

✅ Testing

The workflow repository contains a small test dataset .tests/integration which can be run like so:

$ cd .tests/integration
$ snakemake -s ../../Snakefile -j1 --configfile config.yaml --use-singularity

🚀 Usage

To use this module in your workflow, follow the description in the snakemake docs. Add the module to your Snakefile like so:

module prealignment:
    snakefile:
        github(
            "hydra-genetics/prealignment",
            path="workflow/Snakefile",
            tag="v1.1.0",
        )
    config:
        config


use rule * from prealignment as prealignment_*

Output files

The following output files should be targeted via another rule:

File	Description
prealignment/merged/{sample}_{type}_fastq1.fastq.gz	Merged and possibly trimmed forward reads
prealignment/merged/{sample}_{type}_fastq2.fastq.gz	Merged and possibly trimmed reverse reads
prealignment/sortmerna/{sample}_{type}.fq.gz	combined forward and reverse reads without rRNA sequences

🧑‍⚖️ Rule Graph

Trim and merge fastq

Only merge fastq