Compare Assemblies

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