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Transcript assembly pipeline

The transcript assembly workflow performs genome guided assembly of transcripts. Reads (parameter: reads), either single-end (parameter: single-end: true) or paired-end (parameter: single-end: false), are adapter-trimmed (FastP) and then aligned (Hisat2) against a genome (parameter: genome). Transcripts are constructed using StringTie.

Quick start

Run workflow using the singularity profile:

params.yml:

subworkflow: 'transcript_assembly'
reads: '/path/to/reads*_{R1,R2}.fastq.gz'
genome: '/path/to/genome.fasta'
single_end: false
outdir: '/path/to/save/results'

Command line:

nextflow run NBISweden/pipelines-nextflow \
    -profile singularity \
    -params-file params.yml

Parameters

  • reads: Path to reads.
  • genome: Path to genome.
  • single_end: True if reads are single end reads, false if paired end (default: false).
  • outdir: Path to save results.
  • skip_trimming: True if trimming should be skipped (default: false).

Tool specific parameters

In these workflows, the Nextflow process directive ext.args is used to inject command line tool parameters directly to the shell script. These command line tool parameters can be changed by overriding the ext.args variable for the respective process in a configuration file.

nextflow.config:

process {
    // Override FASTP command line options
    withName: 'FASTP' {
        ext.args   = '-Q -L'
    }
}

See Transcript Assembly modules config for the default tool configuration.

Workflow Stages

  1. Read QC.
    • FastQC: Reads properties are summarised and checked for common issues relating to sequence content and quality.
  2. Read trimming (optional).
    • Fastp: Reads are trimmed for adapter read-through and a QC summary is then provided.
  3. Guided assembly.
    • Hisat2 Build: Builds an index database for the input genome.
    • Hisat2: Align trimmed reads to the genome.
    • Stringtie: Assemble transcripts from the aligned reads.
  4. Summary report.
    • MultiQC: Provide a consolidated report of the statistics from each previous tool.