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Protocols

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 citations

 (673)
library_books

Comparative Genomics Reveals the Core Gene Toolbox for the Fungus Insect Symbiosis

2018
MBio
PMCID: 5954228
PMID: 29764946
DOI: 10.1128/mBio.00636-18

[…] re/) 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 se […]

library_books

Genome Sequencing and Analysis of the Peanut B Genome Progenitor (Arachis ipaensis)

2018
Front Plant Sci
PMCID: 5943715
PMID: 29774047
DOI: 10.3389/fpls.2018.00604

[…] na (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 distribu […]

call_split

Whole genome de novo sequencing reveals unique genes that contributed to the adaptive evolution of the Mikado pheasant

2018
GigaScience
PMCID: 5941149
PMID: 29722814
DOI: 10.1093/gigascience/giy044
call_split See protocol

[…] 0.3”) [], SGA (version 0.10.13; parameters: “assemble -m 125 -d 0.4 -g 0.1 -r 10 -l 200”) [], and SOAPdenovo (version 2.04; parameters: “-K 47 -R”) [] were also used to assemble contigs. We employed SSPACE (SSPACE, RRID:SCR_005056, version 3.0; parameter: “-z 300”) [] to construct scaffolds for the draft genome. In this step, mate pair libraries with 35 bases from the 5' end of both reads were us […]

library_books

Comparative genomics of the nonlegume Parasponia reveals insights into evolution of nitrogen fixing rhizobium symbioses

2018
Proc Natl Acad Sci U S A
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 are […]

call_split

Complete Sequence of the Intronless Mitochondrial Genome of the Saccharomyces cerevisiae Strain CW252

2018
Genome Announc
PMCID: 5920167
PMID: 29700138
DOI: 10.1128/genomeA.00219-18
call_split See protocol

[…] 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. A […]

library_books

Genome Sequence of the Brown Rot Fungal Pathogen Monilinia laxa

2018
Genome Announc
PMCID: 5920163
PMID: 29700136
DOI: 10.1128/genomeA.00214-18

[…] on 3.9.0 software () with default settings. For this step, only the paired-end library was used. Prior to this, all libraries were trimmed using Trimmomatic version 0.36 (). Scaffolding was done with SSPACE version 3.0 () with default settings and employing both libraries. Scaffolds with a size below 1 kb were removed. The final version contained a total scaffold number of 619, an N50 value of 124 […]

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

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