Genome Scaffolder

Computational Biology Lab develops a in silico multi-genome scaffolder, that is aimed at improving existing imperfect assemblies by analyzing multiple genome at the same time.

Our method takes as an input several related genomes (some or even all of which may be fragmented) and performs simultaneous co-assembly of all fragmented genomes. The method relies on the evolutionary model, which includes genome rearrangements as well as gene insertions and deletions. Optionally, the method can obtain additional guidance from the information about DNA repeats from a genome assembler, which is then used to reduce the search space and provide more accurate results. We also integrate our method with the MGRA2 ancestral genomes reconstruction software and utilize its multi-genome evolutionary analysis to increase the quality of the genome assembly performed by our method.

Software package is available at GOS-ASM software page.

Any issues / suggestions with respect to this project (both programming and non-programming) shall be reported to We greatly appreciate your feedback!


  • S. Aganezov and M. A. Alekseyev. “Orientation of Ordered Scaffolds”. Proceedings of the 15th Annual RECOMB Satellite Workshop on Comparative Genomics (RECOMB-CG 2017)Lecture Notes in Computer Science 10562 (2017), 179–196. doi:10.1007/978-3-319-67979-2_10
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  • S. Aganezov, N. Sitdykova, AGC Consortium, and M. A. Alekseyev. “Scaffold assembly based on genome rearrangement analysis”. Proceedings of the 13th Asia-Pacific Bioinformatics Conference (APBC 2015)Computational Biology and Chemistry 57 (2015), 46-53. doi:10.1016/j.compbiolchem.2015.02.005