Supporting materials for "SOAPdenovo2 Case Study".

Dataset type: Workflow, Software
Data released on June 09, 2015

Gonzalez-Beltran A; Li P; Zhao J; Thompson M; Avila-Garcia MS; Luo R; Lam T; Lee T; Roos M; Edmunds SC; Sansone S; Rocca-Serra P (2015): Supporting materials for "SOAPdenovo2 Case Study". GigaScience Database. http://dx.doi.org/10.5524/100148

DOI10.5524/100148

The SOAPdenovo2 case study is a reproducibility study aimed at exploring how existing research objects and workflow enactment engines can help assess, record and preserve scientific workflows and associated findings by reviewing a comparison between sequence assembly algorithm performance in the light of development of the SOAPdenovo2 de novo genome assembler. The case study was a joint effort by the GigaScience journal, the Investigation/Study/Assay (ISA) infrastructure, Nanopublication (Nanopub) and Research Object (RO) communities and SOAPdenovo2 de novo genome assembler developers. Included here are the relevant ISA-TAB, linkedISA, nanopubs and Research Object files. For more see the paper and GitHub page.

Additional details

Read the peer-reviewed publication(s):

Luo, R., Liu, B., Xie, Y., Li, Z., Huang, W., Yuan, J., … Wang, J. (2015). Erratum: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience, 4(1). doi:10.1186/s13742-015-0069-2
Luo, R., Liu, B., Xie, Y., Li, Z., Huang, W., Yuan, J., … Wang, J. (2012). SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience, 1(1). doi:10.1186/2047-217x-1-18
González-Beltrán, A., Li, P., Zhao, J., Avila-Garcia, M. S., Roos, M., Thompson, M., … Rocca-Serra, P. (2015). From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics. PLOS ONE, 10(7), e0127612. doi:10.1371/journal.pone.0127612

Related datasets:

doi:10.5524/100148 IsNewVersionOf doi:10.5524/100044

Additional information:

http://isa-tools.github.io/soapdenovo2/

http://gigagalaxy.net/library/browse_libraries?id=f2db41e1fa331b3e





Displaying 1-2 of 2 File(s).
Date Action
June 9, 2015 Dataset publish
October 23, 2015 File ISA-tools-soapdenovo2-v1.0-1-g9eede6f.tar.gz updated
October 23, 2015 File readme.txt updated
July 9, 2018 External Link added : http://gigagalaxy.net/library/browse_libraries?id=f2db41e1fa331b3e
July 10, 2018 Manuscript Link added : 10.1371/journal.pone.0127612