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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 citations

 (4)
library_books

Genomic Features of the Damselfly Calopteryx splendens Representing a Sister Clade to Most Insect Orders

2017
Genome Biol Evol
PMCID: 5381652
PMID: 28137743
DOI: 10.1093/gbe/evx006

[…] a HiSeq 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 repeats and […]

library_books

Gene Family Evolution Reflects Adaptation to Soil Environmental Stressors in the Genome of the Collembolan Orchesella cincta

2016
Genome Biol Evol
PMCID: 4987106
PMID: 27289101
DOI: 10.1093/gbe/evw134

[…] rs 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, Adaptiv […]

library_books

Sparc: a sparsity based consensus algorithm for long erroneous sequencing reads

2016
PeerJ
PMCID: 4906657
PMID: 27330851
DOI: 10.7717/peerj.2016

[…] conducted on a workstation with AMD Opteron 2425 HE CPUs (@ 800 MHz frequency). In some experiments we provide both NGS data and 3GS data. In these ‘hybrid’ settings 50× Illumina assembly contigs by SparseAssembler () are included and the edge weights are increased by b = 5 ∼ 10. 50× Illumina data provides moderate coverage to allow off-the-shelf de Bruijn graph based assemblers to assemble high- […]

library_books

Data compression for sequencing data

2013
PMCID: 3868316
PMID: 24252160
DOI: 10.1186/1748-7188-8-25

[…] ow-coverage 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. Whil […]

Citations

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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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