snakemake_transcriptome_workflow

Workflow for de novo transcriptome assembly from paired-end reads, protein prediction and annotation, and quality checks. It includes:

• Quality check (fastqc)
• De novo transcriptome assembly (Trinity)
• Assembly quality checks (with bowtie2 and support scripts from Trinity)
• Prediction of open reading frames (Transdecoder)
• Functional annotation (with blastp and hmmer)

this workflow needs the following software

Snakemake: https://snakemake.readthedocs.io/en/stable/index.html

To run succefully every step you need to pre-install: FASTQC Trinity Transdecoder BLAST HMMER

Installation can be done using the conda package manager bioconda

usage

From the workflow directory run the example command lines:

Dry-run

snakemake -np --use-conda

Run

snakemake --cores <max_n_cores> -p --use-conda

Generate pipeline diagram

snakemake --dag | dot -Tsvg > dag.svg --use-conda

run new input

• Move new fastq files to input/fastq_file
• Change sample names in config/sample.tsv
• Update resources/databases with those needed to run blast and hmmer