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Genomic Summary

Since version 0.19.0, segul can calculate summary statistics for raw reads and contiguous sequences.

Raw reads​

Supported file formats:

  • Gunzip Compressed FASTQ (.fq.gz/.fastq.gz)
  • Standard FASTQ (.fq/.fastq)

Example

segul read summary -i raw_reads.fq.gz

or using directory input:

segul read summary -d /raw_read_dir

The output file will be saved as default-read-summary.csv in Read-Summary directory.

To specify, the output directory uses the -output or -o argument:

segul read summary -d /raw_read_dir -o read_dir_output

You can also use the --prefix argument to specify the prefix name of the output files:

segul read summary -d /raw_read_dir -o read_dir_output --prefix my_read_summary

SEGUL provides three modes to calculate summary statistics for raw reads:

Minimal: read count only Default: generate essential statistics (see below) Complete: generate all the essential statistics plus summary statistics per position in each read of each FASTQ 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

Contiguous sequences​

Supported file formats:

  • Fasta (fa/fasta)

Example

segul contig summary -i contigs.fa

or using directory input:

segul contig summary -d /contig_read_dir

You can also specify the output directory names and the prefix for the output file names, similar to the read summary above.

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