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Data released on December 13, 2012

Workflow, Software

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

Luo, R; Liu, B; Xie, Y; Li, Z; Huang, W; Yuan, J; He, G; Chen, Y; Pan, Q; Liu, Y; Tang, J; Wu, G; Zhang, H; Shi, Y; Liu, Y; Yu, C; Wang, B; Lu, Y; Han, C; Cheung, D; Yiu, SM; Liu, G; Zhu, X; Peng, S; Li, Y; Yang, H; Wang, J; Lam, TW; 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 RIS BibTeX Text

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: GigaGalaxy.net/

Related manuscripts:

doi:10.1186/2047-217X-1-18 (PubMed: 23587118)

Related datasets:

doi:10.5524/100044 Compiles doi:10.5524/100038

Additional information:

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

http://soapdenovo2.sourceforge.net/

http://gigagalaxy.net

Samples:

Sample ID Taxonomic ID Common name Genbank name Scientific name Sample attributes
YH 9606 Human human Homo sapiens

Files (FTP site) (Aspera):Aspera user name: gigadb , password: gigadb Table Settings
Items per page:

File Name Sample ID File Type File Format Size Release Date

README.pdf

Readme PDF 1 6 237555231.99 KB 2012-12-13

Assemblathon1_pipeline.tgz

Software UNKNOWN 2 8 1051006710.02 MB 2012-12-13

Bombus_impatiens_pipeline.tgz

Software UNKNOWN 2 7 51307974.89 MB 2012-12-13

Rhodobacter_sphaeroides_pipeline.tgz

Software UNKNOWN 2 7 51244964.89 MB 2012-12-13

Staphylococcus_aureus_pipeline.tgz

Software UNKNOWN 2 7 45450614.33 MB 2012-12-13

YH_pipeline.tgz

YH Software UNKNOWN 2 7 73398827 MB 2012-12-13

readme.txt

Readme TEXT 1 3 3000.29 KB 2012-12-13

isa-tab.zip

ISA-Tab TEXT 1 4 63556.21 KB 2014-08-12