.. _backbone-label:

##########################
 Nf-core-denovotranscript
##########################

**************
 Introduction
**************

nf-core/denovotranscript is a bioinformatics pipeline for de novo
transcriptome assembly of paired-end short reads from bulk RNA-seq. It
takes a samplesheet and FASTQ files as input, perfoms quality control
(QC), trimming, assembly, redundancy reduction, pseudoalignment, and
quantification. It outputs a transcriptome assembly FASTA file, a
transcript abundance TSV file, and a MultiQC report with assembly
quality and read QC metrics.

**********
 Versions
**********

-  1.0.0
-  1.1.0

**********
 Commands
**********

-  denovotranscript

*************
 Example job
*************

Adjust slurm options based on job requirements (`slurm cheat sheet
<https://slurm.schedmd.com/pdfs/summary.pdf>`_):

.. code::

   #!/bin/bash
   #SBATCH -p partitionName  # batch, gpu, preempt, mpi or your group's own partition
   #SBATCH -t 1:00:00  # Runtime limit (D-HH:MM:SS)
   #SBATCH -N 1   # Number of nodes
   #SBATCH -n 1   # Number of tasks per node
   #SBATCH -c 4   # Number of CPU cores per task
   #SBATCH --mem=8G       # Memory required per node
   #SBATCH --job-name=nf-core-denovotranscript    # Job name
   #SBATCH --mail-type=FAIL,BEGIN,END     # Send an email when job fails, begins, and finishes
   #SBATCH --mail-user=your.email@tufts.edu       # Email address for notifications
   #SBATCH --error=%x-%J-%u.err   # Standard error file: <job_name>-<job_id>-<username>.err
   #SBATCH --output=%x-%J-%u.out  # Standard output file: <job_name>-<job_id>-<username>.out

   module purge   ### Optional, but highly recommended.
   module load nf-core-denovotranscript/XXXX      ### Latest version is recommended.