SSPACE-LongRead protocols

SSPACE-LongRead computational protocol

SSPACE-LongRead specifications


Unique identifier OMICS_04686
Name SSPACE-LongRead
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Biological technology Pacific Biosciences
Operating system Unix/Linux
Programming languages C++, Perl
Computer skills Advanced
Stability Stable
Maintained Yes


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Publication for SSPACE-LongRead

SSPACE-LongRead IN pipelines

PMCID: 5571409
PMID: 28839023
DOI: 10.1128/genomeA.00829-17

[…] version 1.2 (6). the final assembled genome consisted of 451 mbp in 4,577 contigs, with 12.7× mean coverage. the largest contig size was 3,055,912 bp. scaffolds (2,396) were generated using sspace-longread (7). the n50 of the contigs was 250,325 bases, and the n50 of the scaffolds was 606,288 bases. the g+c content of the sf9 genome was 36.53%. the size of the sf9 genome […]

PMCID: 4536676
PMID: 26272565
DOI: 10.1128/genomeA.00876-15

[…] and 228-fold average coverage, was assembled using the mira software version 3.0 (16) and the assembled contigs were curated using the lasergene software. the curated contigs were extended using the sspace-longread software using the default parameters (17). the final draft of the synechococcus sp. gfb01 genome consisted of 125 contigs with a total size of 2,339,812 bp and a g+c content […]

SSPACE-LongRead institution(s)
BaseClear BV, Genome analysis and technology department, Leiden, Netherlands
SSPACE-LongRead funding source(s)
This research was partially funded by the WBSO (BaseClear grant SO201305).

SSPACE-LongRead review

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Anonymous user #874

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Too slow (very very very) at the last writing step.
But there are no choice.