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Velvet-SC | De novo assembly of single-cell bacterial genomes from short-read data sets

An approach tailored package for single cell Illumina sequences that incorporates a progressively increasing coverage cutoff. Velvet-SC allows variable coverage datasets to be utilized effectively with assembly of E. coli and S. aureus single cell reads capturing >91% of genes within contigs, approaching the 95% captured from a multi-cell E. coli assembly. It assembles a single cell genome of the uncultivated SAR324 clade of Deltaproteobacteria, a cosmopolitan bacterial lineage in the global ocean. Velvet-SC enable acquisition of genome assemblies for individual uncultivated bacteria, providing cellspecific genetic information absent from metagenomic studies.

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Velvet-SC classification

  • Eubacteria
    • Escherichia coli
    • Staphylococcus aureus

Velvet-SC specifications

Unique identifier:
Software type:
Restrictions to use:
Input format:
fasta, fastq, fasta.gz, fastq.gz, sam, bam, eland, Gerald
Output format:
fasta, AFG, TXT
Computer skills:
Velvet Single Cell
Command line interface
Input data:
Sequence files
Output data:
contigs, statistics, assembly information
Operating system:

Velvet-SC distribution


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University of California, San Diego, Department of Computer Science, La Jolla, CA, USA; J. Craig Venter Institute, San Diego, CA, USA; University of California, San Diego, Department of Mathematics, La Jolla, CA, USA; J. Craig Venter Institute, Chinakville, MD, USA; Illumina Cambridge Ltd., Chesterford Research Park, Saffron Walden, UK

Funding source(s)

This work was partially supported by grants from the National Human Genome Research Institute (NIH-2R01 HG003647) and the Alfred P. Sloan Foundation (Sloan Foundation-2007-10-19), and by a grant from the National Institutes of Health (NIH grant 3P41RR024851-02S1).

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