Basic Nanopore QC

A generic pipeline that can be run on an arbitrary set of Oxford Nanopore sequence files, regardless of the project or organism of interest.

• Sequence quality information

Analyses

• nanoq: Collect sequence QC stats

Usage

nextflow run BCCDC-PHL/basic-nanopore-qc \
  [--prefix 'prefix'] \
  --fastq_input <your fastq input directory> \
  --outdir <output directory>

Output

A single output file in .csv format will be created in the directory specified by --outdir. The filename will be basic_qc_stats.csv. If a prefix is provided using the --prefix flag, it will be prepended to the output filename, for example: prefix_basic_qc_stats.csv.

The output file includes the following headers:

sample_id
reads
bases
n50
longest
shortest
mean_length
median_length
mean_quality
median_quality