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de novo statistics summary

Lauren Coombe edited this page Oct 26, 2023 · 1 revision

ntSynt provides the script analysis_scripts/denovo_synteny_block_stats.py, which can be used to compute fast de novo statistics on the computed synteny blocks.

Usage:

usage: denovo_synteny_block_stats.py [-h] --tsv TSV --fai FAI [FAI ...]

Compute de novo stats on synteny blocks

optional arguments:
  -h, --help           show this help message and exit
  --tsv TSV            ntSynt synteny block file
  --fai FAI [FAI ...]  FAI files for the compared genomes

Output columns:

Column Meaning
Number_blocks Total number of synteny blocks
Number_blocks_all_asm Total number of synteny blocks that include regions from all input genomes
Average_coverage Average synteny coverage (%)
Average_coverage_all_asm Average synteny coverage (%), only considering synteny blocks that include regions from all input genomes
Average_length Average synteny block length (bp)
Median_length Median synteny block length (bp)
Total_length Total length of all blocks, divided by the number of genomes
NG50_length Average synteny block NG50 length (bp)
N50_length Average synteny block N50 length (bp)
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