SSPACE protocols

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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

 (139)
2018
PMCID: 5754496
PMID: 29301887
DOI: 10.1128/genomeA.01416-17

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

2018
PMCID: 5754502
PMID: 29301893
DOI: 10.1128/genomeA.01429-17

[…] 55, 77, 99, and 127). contigs shorter than 500 bp or that comprised fewer than four reads were subsequently filtered out of the assembly. assembly improvement was attempted using a combination of sspace and gapfiller ()., draft assembly of the whole genome yielded 78 contigs, with an n50 value of 333,942 bp. the genome of bjb412 is predicted to be 6,786,668 bp in length, which is comparable […]

2018
PMCID: 5764929
PMID: 29326205
DOI: 10.1128/genomeA.01354-17

[…] of the genome. the resulting sequences were de novo assembled using the clc genomics workbench version 8.5.1. the contig sequences were corrected with pilon version 1.11 () and linked using the sspace premium scaffolder version 2.3 (). gapped regions within the scaffolds were partially closed in an automated manner using gapfiller version 1.10 (). annotation and identification of open […]

2018
PMCID: 5773145
PMID: 29343217
DOI: 10.1186/s12864-018-4440-4

[…] insert size). the paired-end reads were assembled into longer contigs using velvet version 1.0.12 [], with an optimized k-mer size of 65. the pre-assemblies were used to construct scaffolds with the sspace program []., the c. cacaofunesta genes were predicted by combining evidence retrieved from rna-seq data and comparative gene finding. rna-seq reads were obtained via in vitro laboratory […]

2018
PMCID: 5786695
PMID: 29371369
DOI: 10.1128/genomeA.01565-17

[…] to be 5.51%. a total of 1,116,202 paired-end reads were filtered per the read qualities. the reads were then assembled using the spades software (). contigs obtained were combined by use of sspace () and assisted by manual finishing and gapfiller (). this yielded a 7,306,349-bp draft genome sequence with a 66.35% gc content, composed of 14 scaffolds and 14 contigs. open reading frames […]


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SSPACE in publications

 (555)
PMCID: 5954228
PMID: 29764946
DOI: 10.1128/mBio.00636-18

[…] and were quality checked using fastqc v0.11.4 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). genomes were assembled with ray v2.3.1 (). the scaffolds of s. simulii were built using sspace (). satellites, simple repeats, and low-complexity sequences were annotated with repeatmasker v4.0.5 (http://www.repeatmasker.org) and tandem repeat finder v4.07b (), corresponding to fungal […]

PMCID: 5943715
PMID: 29774047
DOI: 10.3389/fpls.2018.00604

[…] (san diego, usa)., soapdenovo2 (version 2.04.4) (luo et al., ) was employed with optimized parameters to construct contigs and original scaffolds as previous described (chen et al., ). subsequently, sspace (version 2.0) (boetzer et al., ) was used to link the scaffolds constructed by the soapdenovo2 as previous described (chen et al., )., the genome size was estimated based on the 17 k-mer […]

PMCID: 5941149
PMID: 29722814
DOI: 10.1093/gigascience/giy044

[…] using only short-read sequencing technology. we assert that the high coverage of our sequencing data, differing library insert sizes, and the use of a combination of tools, such as masurca and sspace for assembly and scaffolding, respectively, contributed to high-quality de novo assembly of the mikado pheasant genome with a genome length of approximately 1 gb., recent studies have reported […]

PMCID: 5960304
PMID: 29717040
DOI: 10.1073/pnas.1721395115

[…] cleaned dna sequencing reads were de novo assembled by using allpaths-lg (release 48961) (). after filtering of any remaining adapters and contamination, contigs were scaffolded with two rounds of sspace-standard (v3.0) () with the mate-pair libraries using default settings. we used the output of the second run of sspace scaffolding as the final assembly (full details and parameter choices […]

PMCID: 5920167
PMID: 29700138
DOI: 10.1128/genomeA.00219-18

[…] by trinity () to obtain an estimated coverage of 30×. an assembly of the genome obtained by velvet () with a k-mer size of 55 produced 34 contigs (n50, 3.7 kb), which were subsequently scaffolded by sspace () to obtain 10 contigs (n50, 57.5 kb). some of these scaffolds seemed to be chimeric, since a mapping of the original paired-end reads on this assembly by bwa () displayed only 85% success. […]


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

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