Assembly Reconciliation Tools

Tools

• CISA:

  Lin, S.-H. & Liao, Y.-C. CISA: Contig Integrator for Sequence Assembly of Bacterial Genomes. PLoS ONE 8, e60843 (2013).
  http://sb.nhri.org.tw/CISA/en/Instruction (version 1.3, CISA - 2014.03.04).

• GAA:

  Yao, G. et al. Graph accordance of next-generation sequence assemblies. Bioinformatics 28, 13–16 (2012).
  http://sourceforge.net/projects/gaa-wugi/ (version 1.1).

• GAM_NGS:

  Riccardo Vicedomini, Vezzi, F., Scalabrin, S., Arvestad, L. & Policriti, A. GAM-NGS: genomic assemblies merger for next generation sequencing. BMC Bioinformatics 14, S6 (2013).
  https://github.com/vice87/gam-ngs (version 1.1b).

• GARM:

  Mayela Soto-Jimenez, L., Estrada, K. & Sanchez-Flores, A. GARM: Genome Assembly, Reconciliation and Merging Pipeline. Current Topics in Medicinal Chemistry 14, 418–424 (2014).
  http://garm-meta-assem.sourceforge.net/ (version 0.7.3).

• Metassembler:

  Wences, A. H. & Schatz, M. Metassembler: Merging and optimizing de novo genome assemblies. bioRxiv 016352 (2015). doi:10.1101/016352.
  http://sourceforge.net/projects/metassembler/ (version 1.2).

• Mix:

  Soueidan, H. et al. Finishing bacterial genome assemblies with Mix. BMC Bioinformatics 14, 1–11 (2013).
  https://github.com/cbib/MIX

• Zorro:

  Argueso, J. L. et al. Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production. Genome Res 19, 2258–2270 (2009).
  http://lge.ibi.unicamp.br/zorro/ (version 2.2).