Software and supporting material for “SOAPdenovo2: An empirically improved memory-efficient short read de novo assembly”

Dataset type: Workflow, Software
Data released on December 13, 2012

Chen Y; Cheung D; Han C; He G; Huang W; Lam TW; Li Y; Li Z; Liao X; Liu B; Liu G; Liu Y; Liu Y; Lu Y; Luo R; Pan Q; Peng S; Shi Y; Tang J; Wang B; Wang J; Wu G; Xiaoqian Z; Xie Y; Yang H; Yiu S; Yu C; Yuan J; Zhang H; Wang J (2012): Software and supporting material for “SOAPdenovo2: An empirically improved memory-efficient short read de novo assembly” GigaScience Database. http://dx.doi.org/10.5524/100044

DOI10.5524/100044

SOAPdenovo2 is the latest de novo genome assembly package from BGI’s SOAP (short oligonucleotide analysis package) suite of tools (homepage here: http://soap.genomics.org.cn/). Compared to SOAPdenovo1, this new version has the advantage of a new algorithm design that reduces memory consumption in graph construction, resolves more repeat regions in contig assembly, increases coverage and length in scaffold construction, improves gap closure, and is optimized for large genomes.
Using new sequencing data from the YH (Homo sapiens) diploid genome – the first sequenced Han Chinese individual, an updated assembly was produced (see dataset here: doi:10.5524/100038), with the N50 scores for the contig and scaffold being 3-fold and 50-fold longer, respectively, than the first published version. The genome coverage increased from 81.16% to 93.91%, and memory consumption was ~2/3 times lower during the point of largest memory consumption.
Benchmarking with Assemblathon1 and GAGE datasets shows that SOAPdenovo2 greatly surpasses its predecessor SOAPdenovo1 and is competitive to other assemblers on both assembly length and accuracy.
In order to facilitate readers to repeat and recreate these findings, configured packages with the compressed pipelines containing all of the necessary shell scripts and tools are available from the BGI FTP server (ftp://public.genomics.org.cn/BGI/SOAPdenovo2).
The latest version of SOAPdenovo2 is available from Sourceforge: http://soapdenovo2.sourceforge.net/
These pipelines are available from our data platform as Galaxy workflows: http://galaxy.cbiit.cuhk.edu.hk/

Additional details

Read the peer-reviewed publication(s):

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 (PubMed: 23587118)

Related datasets:

doi:10.5524/100044 Compiles doi:10.5524/100038
doi:10.5524/100044 IsPreviousVersionOf doi:10.5524/100148 (It is a more recent version of this dataset)


There is a new version of this dataset available at: DOI: 10.5524/100148

Additional information:

http://soap.genomics.org.cn/

http://soapdenovo2.sourceforge.net/

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





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
YH9606HumanhumanHomo sapiens
Displaying 1-1 of 1 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
SoftwareUNKNOWN10.02 MB2012-12-13
SoftwareUNKNOWN4.89 MB2012-12-13
ISA-TabTEXT6.21 KB2014-08-12
ReadmePDF231.99 KB2012-12-13
ReadmeTEXT0.29 KB2012-12-13
SoftwareUNKNOWN4.89 MB2012-12-13
SoftwareUNKNOWN4.33 MB2012-12-13
YHSoftwareUNKNOWN7 MB2012-12-13
Displaying 1-8 of 8 File(s).
Funding body Awardee Award ID Comments
Shenzhen Key Laboratory of Trans-omics Biotechnologies CXB201108250096A
National Natural Science Foundation of China 90612019
National High Technology Research and Development Program of China-863 program 2012AA02A201
State Key Development Program for Basic Research of China-973 Program 2011CB809203
Shenzhen Municipal Government of China JC201005260191A
Date Action
October 16, 2015 File Assemblathon1_pipeline.tgz updated
July 9, 2018 External Link updated : http://gigagalaxy.net/library/browse_libraries?sort=name&f-description=All&f-name=All&operation=browse&id=f2db41e1fa331b3e
July 9, 2018 External Link updated : http://gigagalaxy.net/library/browse_libraries?id=f2db41e1fa331b3e