Routine Nanopore QC

A generic pipeline that can be run routinely on all Illumina sequence runs, regardless of the project or organism of interest.

• Sequence quality information
• Possible contamination

Analyses

• nanoq: Basic sequence stats including total reads, total bases, read N50 and read quality.
• kraken2: Taxonomic classification of reads.

Usage

nextflow run BCCDC-PHL/routine-nanopore-qc \
  --kraken2_db /path/to/kraken2_db \
  --fastq_input /path/to/reads \
  --outdir /path/to/output_directory

Outputs

Nanoq report:

sample_id
reads
bases
n50
longest
shortest
mean_length
median_length
mean_quality
median_quality

Species-level Kraken Report:

sample_id
percent_seqs_in_clade
num_seqs_in_clade
num_seqs_this_taxon
rank_code
ncbi_taxonomy_id
taxon_name