Python script for comparing two genome assemblies
- get scaffolding mapping using minimap2 (done)
- write out mapping results (done)
- get scaffold statistics: length, gaps, repeat content, GC content (done)
- support cases with partial synteny between assemblies (to do)
- get contig metrics (to do)
usage: compareAssemblies.py [-h] -r ASM1FILENAME -q ASM2FILENAME
[-m MINGAPSIZE] [-n MINQUERYLEN] [-o OUTPUTPREFIX]
[-d]
compare assemblies with minimap2
optional arguments:
-h, --help show this help message and exit
-r ASM1FILENAME input assembly 1 (ref) fasta
-q ASM2FILENAME input assembly 2 (query) fasta
-m MINGAPSIZE minimum gap size, default=25
-n MINQUERYLEN minimum sequence length in assembly 2 (query), default=20Mb
-o OUTPUTPREFIX output prefix, default=output
-d turn off saving minimap2 results