Skip to main content

NanoStat

note

Reports various statistics for long read dataset in FASTQ, BAM, or albacore sequencing summary format (supports NanoPack; NanoPlot, NanoComp)

https://github.com/wdecoster/nanostat/, https://github.com/wdecoster/nanoplot/

Programs are part of the NanoPack family for summarising results of sequencing on Oxford Nanopore methods (MinION, PromethION etc.)

NanoStat module for parsing statistics from Oxford Nanopore sequencing data.

By default, only the Read N50 metric is shown in the General Statistics table, with all other metrics hidden. You can customize which metrics appear in the General Statistics table using the general_stats_columns configuration option in your MultiQC config file.

For example, to show number of reads, mean read length and median quality for FASTQ data:

general_stats_columns:
  nanostat:
    columns:
      Number of reads_fastq:
        title: "# Reads"
        description: "Number of reads"
        hidden: false
      Mean read length_fastq:
        title: "Mean Length"
        description: "Mean read length"
        hidden: false
      Median read quality_fastq:
        title: "Median Quality"
        description: "Median read quality"
        hidden: false

Available metrics that can be added to General Statistics (append _fastq, _aligned, _fasta or _seq summary depending on the data type):

  • Active channels - Number of active channels
  • Median read length - Median read length (bp)
  • Mean read length - Mean read length (bp)
  • Read length N50 - Read length N50
  • Median read quality - Median read quality (Phred scale)
  • Mean read quality - Mean read quality (Phred scale)
  • Median percent identity - Median percent identity
  • Average percent identity - Average percent identity
  • Number of reads - Number of reads
  • Total bases - Total number of bases
  • Total bases aligned - Total number of aligned bases

Each metric can be customized with the following options:

  • title - Column title
  • description - Column description
  • hidden - Whether to hide the column by default
  • scale - Color scale for the column
  • format - Number format
  • min - Minimum value for the color scale
  • max - Maximum value for the color scale
  • suffix - Suffix to add to values
  • shared_key - Share color scale with other columns

File search patterns​

nanostat:
  contents_re: Metrics\s+dataset\s*
  max_filesize: 4096
  num_lines: 1
nanostat/legacy:
  contents_re: General summary:\s*
  max_filesize: 4096
  num_lines: 1