SSPACE pipeline

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

 (24)
2018
PMCID: 5946948

[…] 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 […]

2018
PMCID: 5754496

[…] 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) […]

library_books

IMA Genome-F 8

2017
PMCID: 5729718

[…] was used for quality and adapters trimming of pair-end reads. the genome was assembled from trimmed reads using spades v. 3.10 (bankevich et al. 2012) and was further placed into scaffolds using sspace standard v. 3.0 (boetzer et al. 2011). gaps were filled or reduced with gapfiller v. 1.10 (boetzer & pirovano 2012). several runs of genome assembly were conducted using different […]

2017
PMCID: 5687760

[…] technology, bangalore india). the spades-3.5.0 was used for sequence assembly followed by the filling of gaps. finally, scaffolding of assembled contigs and clustering were carried out with sspace and cap3 programs, respectively [16–17]., the assembled scaffolds were annotated using mitos web-server to predict the location of protein coding regions/genes, trnas, rrnas and secondary […]

2017
PMCID: 5687760

[…] 28,69,153 high quality reads were processed for scaffold preparation. these reads were used for mitogenome scaffold preparation through de novo assembly of sequenced contigs using spades-3.5.0, sspace and cap3 program. finally, a scaffold of 15,272 bp length was obtained which represents the whole mitogenome sequence of a. assamensis., the annotated mitochondrial genome of a. assamensis […]

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

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