SSPACE protocols

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SSPACE computational protocol

SSPACE specifications

Information


Unique identifier OMICS_00050
Name SSPACE
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Pre-assembled contig sequence data, NGS paired-read data
Input format FASTA, FASTQ
Output data Final scaffolds
Output format FASTA
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for SSPACE

SSPACE IN pipelines

 (45)
2018
PMCID: 5754496
PMID: 29301887
DOI: 10.1128/genomeA.01416-17

[…] of any outliers. reads mapping to contigs within each genome bin were extracted and reassembled using spades (11) with the “-careful” flag enabled. a final scaffolding step was performed using sspace (12). final draft genome completeness and contamination was assessed using checkm (13). the final draft genome was annotated using the ncbi prokaryotic genome annotation pipeline (pgap) (14) […]

2018
PMCID: 5886536
PMID: 29621340
DOI: 10.1371/journal.pone.0195461

[…] adding the pacbio data using the pbjelly software, the contig n50 increased to 149.7 kb and the scaffold n50 increased to 1.138 mb. after an additional incorporation of the same pacbio data using sspace, the contig n50 increased again to 165.6 kb and the scaffold size increased to 2.192 mb. these scaffolds were then ordered using two genetic maps and two reference genomes (rainbow trout […]

2018
PMCID: 5902842
PMID: 29661190
DOI: 10.1186/s12864-018-4656-3

[…] with an n50 of 275 bases [26]. assembly of these fragments using a long insert library (roche 454 gs-flx – 4 kb) using newbler produced 39,868 contigs. subsequent stepwise scaffolding using sspace2 [27] with illumina long-range insert libraries of 4, 9 and 13 kb yielded 39,825, 8688 and 3887 scaffolds, respectively. after two iterations of gap closure the final assembly consisted […]

2018
PMCID: 5936940
PMID: 29765675
DOI: 10.1098/rsos.172212

[…] [57] with k-mers of 61 for l. guyanensis, 43 for l. naiffi and 43 for the l. braziliensis control optimized for eachlibrary., the initial contigs were scaffolded using read pair information with sspace [58] to yield 2800 l. guyanensis scaffolds with an n50 of 95.4 kb, 6530 l. naiffi scaffolds with an n50 of 24.3 kb, and 3782 l. braziliensis scaffolds with an n50 of 20.6 kb (table 2). […]

2018
PMCID: 5946948
PMID: 29688346
DOI: 10.1093/gigascience/giy046

[…] with insert size of 2 kb, 5 kb, 10 kb, and 20 kb were used to assemble the scaffolds by soapdenovo. the sequence data derived from the library with 40 kb insert were used to build scaffolds with sspace version 1.1 software [17]., to assess assembly quality and completeness, high quality reads from short-insert-size libraries (75 bp read lengths) were aligned to the assembly with the bwa […]

SSPACE institution(s)
BaseClear BV; Einsteinweg, Leiden, Netherlands

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