Sealer protocols

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Sealer specifications

Information


Unique identifier OMICS_09432
Name Sealer
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Stability Stable
Requirements
Google sparsehash
Maintained Yes

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Maintainer


  • person_outline Inanc Birol <>

Publication for Sealer

Sealer in pipelines

 (2)
2017
PMCID: 5347234
PMID: 28280014
DOI: 10.1128/genomeA.00022-17

[…] the sequences from the microbe, the reads were down-sampled to 400 mb, thereby reducing sequences originating from relatively minor species, and assembled using velvet, followed by gap-closing with sealer (, ). the resulting draft genome of strain emtcatb1 is 1.84 mb (g+c content, 67.2%) contained in a single circular scaffold with no gap, representing a circular chromosome. the scaffold […]

2017
PMCID: 5597760
PMID: 28912319
DOI: 10.1128/genomeA.00963-17

[…] with miseq reads using unicycler (). the assembly was polished with unicycler_polish using all sequence reads and scaffolded with links v1.8.5 () using nanopore reads. assembly gaps were closed with sealer v1.5.2 using miseq reads exclusively (). the resulting assembly was aligned against other m. chimaera genomes using mauve 2.3.1 (). genomic features were identified and annotated using […]


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Sealer in publications

 (13)
PMCID: 5748696
PMID: 29232881
DOI: 10.3390/genes8120378

[…] with cobbler using abyss contigs was applied (same parameters as above). the genome scaffolding steps yielded an improved scaffold n50 length of 19.59 mbp. further improvement was achieved using sealer (version 2.0.2, parameter -k at 60–200, step 10) [], which used sequence contigs from the abyss k100 assembly to close an additional 1059 sequence gaps. , the final assembly () comprises 2.327 […]

PMCID: 5748697
PMID: 29232880
DOI: 10.3390/genes8120379

[…] in all, the scaffolding steps yielded an improved scaffold n50 length of 38.45 mbp and provided the closure of 6298 gaps incorporating 32.2 mbp of the sequence. further improvement was achieved with sealer (version 2.0.2, canada’s michael smith genome sciences centre); parameter -k at 90–200, step 10) [], using sequence contigs from the abyss k100 assembly to further close gaps. in all, sealer […]

PMCID: 5737505
PMID: 29194487
DOI: 10.1093/gbe/evx248

[…] from 65 through 200. each assembly was further scaffolded with abyss using the megahit-derived transcripts. the assembly with the highest e-size () was retained for improvement and analysis. abyss sealer v2.0.1 () was used to fill gaps in the retained assembly using every tenth kmer starting at 100 and decreasing to 30. pilon v1.22 () polished the resulting gap-filled assembly using […]

PMCID: 5681567
PMID: 29127278
DOI: 10.1038/s41467-017-01316-7

[…] by the ng50 length, and further recovery of 38 complete busco genes (supplementary table ).table 1see methods section for details , see methods section for details, the automated gap closing tool sealer was used three times during the assembly process. first, prior to the rounds of rescaffolding to increase the amount of resolved sequence available to inform the scaffolding algorithms, […]

PMCID: 5597760
PMID: 28912319
DOI: 10.1128/genomeA.00963-17

[…] with miseq reads using unicycler (). the assembly was polished with unicycler_polish using all sequence reads and scaffolded with links v1.8.5 () using nanopore reads. assembly gaps were closed with sealer v1.5.2 using miseq reads exclusively (). the resulting assembly was aligned against other m. chimaera genomes using mauve 2.3.1 (). genomic features were identified and annotated using […]


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Sealer institution(s)
Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada

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