Genomic Contig Summary

segul contig summary calculates summary statistics for assembled contigs in FASTA format. For raw reads, see Genomic Read Summary.

Input formats

• Gunzip Compressed FASTA (.fa.gz/.fasta.gz)
• Standard FASTA (.fa/.fasta)

Usage

segul contig summary -i contigs.fa

or using directory input:

segul contig summary -d /contig_read_dir

Use --output (or -o) to set the output directory and --prefix to set the prefix of the output files:

segul contig summary -d /contig_read_dir -o contig_output --prefix my_contig_summary

Statistics

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

All options

Option	Description
-d, --dir	Directory with contig files
-i, --input	Contig files. Allows wildcards
-f, --input-format	Input format: auto (default), fasta, or gzip
-o, --output	Output directory. Default: Contig-Summary
--prefix	Prefix of the output files
--force	Overwrite an existing output directory
--log	Log file path. Default: segul.log