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!


  1. S. Aganezov and M. A. Alekseyev. “Multi-genome Scaffold Co-Assembly Based on the Analysis of Gene Orders and Genomic Repeats”. Proceedings of the 12th International Symposium on Bioinformatics Research and Applications (ISBRA 2016), Lecture Notes in Computer Science 9683 (2016), 237–249. doi:10.1007/978-3-319-38782-6_20
  2. Y.-C. Liu, S.-D. Hsu, C.-H. Chou, W.-Y. Huang, Y.-H. Chen, C.-Y. Liu, G.-J. Lyu, S.-Z. Huang, S. Aganezov, M. A. Alekseyev, C.-D. Hsiao, and H.-D. Huang. “Transcriptome sequencing based annotation and homologous evidence based scaffolding of Anguilla japonica draft genome”. BMC Genomics 17:Suppl 1 (2016), 13. doi:10.1186/s12864-015-2306-6
  3. D. E. Neafsey, R. M. Waterhouse, M. R. Abai, S. S. Aganezov, M. A. Alekseyev et al. “Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes”, Science 347:6217 (2015), 1258522. doi:10.1126/science.1258522