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Genomic Summary

This feature provides summary statistics for sequence reads and contiguous sequences (contigs).

Sequence Read Summary Statistics​

Steps for Sequence Read Summary Statistics​

  1. Select the Genomic button from the navigation bar.
  2. Select Summarize genomic reads from the dropdown menu.
  3. Add the input files by clicking the Add file button. On desktop platforms, you can also input a directory by clicking the Add directory button. The app will look for matching files in the directory.
  4. All the input files will be displayed in the input tab bar. You can remove the file by clicking the Remove button. Removing the file will only remove it from input list and not from the file system.
  5. Select the summary mode.
  6. Click the Run button labeled Sequence read summary statistics to start the task.
  7. Share the output (optional).

Summary Mode​

The app supports the following summary modes:

  • Minimal: read count only
  • Default: generate essential statistics (see below)
  • Complete: generate all the essential statistics plus summary statistics per position in read for each file.

Essential statistics for raw reads​

  • Number of reads
  • Number of bases
  • Mean read length
  • Minimum read length
  • Maximum read length
  • GC count
  • GC content
  • AT count
  • AT content
  • A, C, G, T, N count
  • Low quality base count
  • Mean base quality
  • Min base quality
  • Max base quality

Contig Summary Statistics​

Steps for Contig Summary Statistics​

  1. Select the Genomic button from the navigation bar.
  2. Select Summarize genomic contigs from the dropdown menu.
  3. Add the input files by clicking the Add file button. On desktop platforms, you can also input a directory by clicking the Add directory button. The app will look for matching files in the directory.
  4. All the input files will be displayed in the input tab bar. You can remove the file by clicking the Remove button. Removing the file will only remove it from input list and not from the file system.
  5. Add the output directory by clicking the Add output directory button. On mobile platforms, the directory will be the default directory for the app.
  6. Click the Run button labeled Contig summary statistics to start the task.
  7. Share the output (optional).

Available statistics for contiguous sequences​

  • Contig count
  • Base count
  • Nucleotide
  • GC content
  • AT content
  • Minimum contig length
  • Maximum contig length
  • Mean contig length
  • Median contig length
  • N50
  • N75
  • N90
  • Contig 750 bp
  • Contig 1000 bp
  • Contig 1500 bp
  • Cumulative length
  • A, C, G, T, N counts