SparseAssembler pipeline

SparseAssembler specifications

Information


Unique identifier OMICS_00032
Name SparseAssembler
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Chengxi Ye <>

Publication for SparseAssembler

SparseAssembler IN pipeline

2017
PMCID: 5381652
PMID: 28137743
DOI: 10.1093/gbe/evx006

[…] 2500 sequencer. all raw reads (∼2.6 billion) are deposited in the ncbi short-read archive (sra) under accession numbers srp075442 (bioproject: prjna315816)., contig assembly was performed using sparseassembler v. 2012-06-15 (ye et al. 2012), and scaffolding was performed on contigs >200 bp in size using sspace v. 3.0 (boetzer et al. 2011). finally, short (<15 kbp) scaffolds […]

SparseAssembler institution(s)
Ecology & Evolution of Plant-Animal Interaction Group, Xishuangbanna Tropical Botanic Garden, Chinese Academy of Sciences, Menglun, Yunnan, China; Ecology, Conservation, and Environment Center, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China; Department of Computer Science and Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD, USA; Computational Biology and Medical Ecology Lab; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China; Ecological Evolution Group, Xishuangbanna Tropical Botanic Garden, Chinese Academy of Sciences, Menglun, Yunnan, China; Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA; School of Biological Sciences, University of East Anglia, Norwich, Norfolk, UK
SparseAssembler funding source(s)
This work was supported in part by Yunnan Province, China [20080A001], and the Chinese Academy of Sciences [0902281081, KSCX2-YW-Z-1027, Y002731079], and also by the US National Science Foundation grant IIS-0812111.

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