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pyScaf

https://github.com/lpryszcz/pyScaf

pyScaf orders contigs from genome assemblies utilising several types of information:

Scaffolding 

In reference-based mode, pyScaf uses synteny to the genome of closely related species in order to order contigs and estimate distances between adjacent contigs.

Contigs are aligned globally (end-to-end) onto reference chromosomes, ignoring:

  • matches not satisfying cut-offs (--identity and --overlap)
  • suboptimal matches (only best match of each query to reference is kept)
  • and removing overlapping matches on reference.

In preliminary tests, pyScaf performed superbly on simulated heterozygous genomes based on C. parapsilosis (13 Mb; CANPA) and A. thaliana (119 Mb; ARATH) chromosomes, reconstructing correctly all chromosomes always for CANPA and nearly always for ARATH (Figures in dropboxCANPA tableARATH table).
Runs took ~0.5 min for CANPA on 4 CPUs and ~2 min for ARATH on 16 CPUs.

Important remarks:

  • Reduce your assembly before (fasta2homozygous.py) as any redundancy will likely break the synteny.
  • pyScaf works better with contigs than scaffolds, as scaffolds are often affected by mis-assemblies (no de novo assembler / scaffolder is perfect...), which breaks synteny.
  • pyScaf works very well if divergence between reference genome and assembled contigs is below 20% at nucleotide level.
  • pyScaf deals with large rearrangements ie. deletions, insertion, inversions, translocations. Note however, this is experimental implementation!
  • Consider closing gaps after scaffolding.