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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) |