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Protocols

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SSAKE specifications

Information


Unique identifier OMICS_00033
Name SSAKE
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for SSAKE

SSAKE in pipelines

 (2)
2017
PMCID: 5905499
PMID: 29253216
DOI: 10.1093/gigascience/gix125

[…] pasa: program to assemble spliced alignment; reapr: recognition of errors in assemblies using paired reads; sine: short interspersed nuclear elements; snp: single nucleotide polymorphism; sspace: ssake-based scaffolding of pre-assembled contigs after extension; te: transposable element., the authors declare that they have no competing interests., this work was supported by competitive grants […]

2016
PMCID: 4913238
PMID: 27320081
DOI: 10.1038/srep28338

[…] kit illumina platforms following the manufacturer’s instructions. the assembly used 7,907,550 reads, or 988.4 mb, of raw data to give a 24410 × coverage of the genome. the reads were assembled using ssake (v3.8) assembly software. the final assembled sequence was searched against the current protein and nucleotide databases (http://www.ncbi.nlm.nih.gov/) using the basic local alignment search […]


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SSAKE in publications

 (42)
PMCID: 5905499
PMID: 29253216
DOI: 10.1093/gigascience/gix125

[…] match the performance achieved in assemblies of homozygous genomes, especially at the contig assembly level []. we thus used the assembled contigs to perform an alternative scaffolding step with ssake-based scaffolding of pre-assembled contigs after extension (sspace, rrid:scr_005056) [] using the error-corrected short fragment reads and the jumping reads. in this approach, genome assembly […]

PMCID: 5207757
PMID: 28045932
DOI: 10.1371/journal.pone.0168397

[…] melanogaster in response to viral infections were sufficient to reconstruct and improve the genomic consensus sequence of the nora virus [] using the paparazzi software [] which is based on the ssake assembler []. in that study, paparazzi improved the consensus sequence and the coverage of the nora virus genome by ~20%, as compared to the previous nora virus reference genome. […]

PMCID: 5596377
PMID: 28898352
DOI: 10.1590/1678-4685-GMB-2016-0230

[…] and is developed to work on the linux operating system., sopra (): this scaffolding tool was designed to improve assemblies generated by velvet () and ssake (), and targets the earlier sequencing platforms from illumina and abi solid. the program parses the read-placing file generated by these assemblers and extracts information […]

PMCID: 5295771
PMID: 27870834
DOI: 10.1038/nsmb.3330

[…] considering that both ectosymbionts and endosymbionts have been reported in ciliates ., several assembly programs were used to generate independent whole-genome assemblies, including abyss , soap , ssake , velvet , celera , 454 newbler v.2.7, and pcap ,. to perform the assembly, we followed the instruction manuals for newbler and celera and the published protocols for other programs. a hybrid […]

PMCID: 5017225
PMID: 27609920
DOI: 10.1128/genomeA.00944-16

[…] version 1.2 (). reads were also aligned to escherichia coli se15 (genbank accession no. nc_013654). the de novo assemblies and alignment-based contigs were merged using gap4 (), scaffolded with ssake-based scaffolding of pre-assembled contigs after extension (sspace) version 2.0 (), and gaps were pcr amplified and sequenced by sanger sequencing. the assembly of a pseudochromosome resulted […]


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SSAKE institution(s)
British Columbia Cancer Agency, Genome Sciences Centre, Vancouver, Canada; J. Craig Venter Institute, Rockville, MD, USA

SSAKE reviews

 (2)
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Ahmed Nabiel

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Desktop
The best short read assembler I could find!
Anonymous user #48's avatar image No country

Anonymous user #48

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Desktop
Ssake is super easy to use and produces accurate results.
It is lightweight and has no dependencies, I highly recommend it. Because it uses coverage info, assemblies are stratified which makes it also suitable for transcriptome and meta genome assemblies. It is not as greedy as most people report, the correct path is chosen no based on longest overlap, but coverage and reads having a matching pairing partner already assembled