SparseAssembler protocols

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SparseAssembler specifications

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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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  • person_outline Chengxi Ye <>

Publication for SparseAssembler

SparseAssembler in pipelines

 (2)
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 (), and scaffolding was performed on contigs >200 bp in size using sspace v. 3.0 (). finally, short (<15 kbp) scaffolds were removed, as these usually contain […]

2017
PMCID: 5645146
PMID: 28968408
DOI: 10.1371/journal.pcbi.1005777

[…] independently for plagiarism detection in schleimer et al. []. for example, msp [] compresses k-mers by hashing them to their 4-mer minimizer to efficiently construct a de bruijn graph for assembly. sparseassembler [] represents the de bruijn graph using only every g-th k-mer in the sequence (and has also been implemented using minimizers). kraken [] uses minimizers to speed up database queries […]

SparseAssembler in publications

 (4)
PMCID: 5425390
PMID: 27889940
DOI: 10.1111/pbi.12674

[…] et al., ). this assembly included illumina pe raw reads and raw pacbio reads. the first step within the analysis involved two rounds of illumina read error correction and subsequent assembly with sparseassembler [beta version; ye et al. ()]. the coverage threshold for both an error and for a correct sparse k‐mer candidate in the correction process was set to 5. in the first round, the k‐mer […]

PMCID: 4987106
PMID: 27289101
DOI: 10.1093/gbe/evw134

[…] in the raw reads were corrected with the sga tool () and duplicates were removed with the fastq-mcf tool (). based on the cleaned illumina reads we estimated the genome size with the bgi method ()., sparseassembler v.1beta () was applied (nodecoveth = 1, edgecovth = 1, k = 21, g = 15, pathcovth = 100) to build contigs based on illumina data and the dbg2olc tool () was used (kmercovth = 2, […]

PMCID: 3868316
PMID: 24252160
DOI: 10.1186/1748-7188-8-25

[…] edges, which normally result in tips, loops or bubbles in the assembly graph, undesirable in the graph for a few reasons, including very high memory requirements. the compact structure of sparseassembler from the cited work was built in less than 2 hours for the human chromosome 14 with the peak memory use of 3 gb. the memory requirement for the whole human genome was below 30 gb. […]

PMCID: 3785575
PMID: 24086547
DOI: 10.1371/journal.pone.0075505

[…] of modern assemblers for a variety of datasets. we compare the prevalent memory-efficient techniques against a typical traditional approach (i.e., velvet []). we compare the following programs: sparseassembler [], gossamer [], minia [] and sga []. all of them are open-source and representative of the recent assembly trends, namely: the efficient construction of large assembly graphs […]

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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