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SSAKE specifications


Unique identifier OMICS_00033
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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SSAKE citations


Genome assembly of the Pink IpĂȘ (Handroanthus impetiginosus, Bignoniaceae), a highly valued, ecologically keystone Neotropical timber forest tree

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 […]


Metavisitor, a Suite of Galaxy Tools for Simple and Rapid Detection and Discovery of Viruses in Deep Sequence Data

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. […]


Approaches for in silico finishing of microbial genome sequences

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 […]


Position dependent termination and widespread obligatory frameshifting in Euplotes translation

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 […]


Draft Genome Sequence of Uropathogenic Escherichia coli Strain NB8

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 […]


Benchmarking of de novo assembly algorithms for Nanopore data reveals optimal performance of OLC approaches

PMCID: 5001211
PMID: 27556636
DOI: 10.1186/s12864-016-2895-8

[…] order to comprehensively evaluate multiple algorithmic frameworks, we included assemblers based on de bruijn graphs (velvet and abyss), overlap layout consensus (olc) (celera) and greedy extension (ssake) approaches. we analyzed the quality, accuracy of the assemblies as well as the computational performance of each of the assemblers included in our benchmark. our analysis unveiled […]

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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

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Ahmed Nabiel

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

Anonymous user #48

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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