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Citations per year

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Staden specifications

Information


Unique identifier OMICS_00894
Name Staden
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C
License BSD 2-clause “Simplified” License
Computer skills Medium
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Staden_Package

Subtools


  • Gap4
  • spin

Versioning


Add your version

Maintainer


  • person_outline James Bonfield <>

Publications for Staden

Staden in pipelines

 (44)
2018
PMCID: 5796565
PMID: 29435100
DOI: 10.1186/s40793-017-0306-7

[…] a total of 221,447,771 bases and represented 41.5-fold genome coverage. these reads were assembled in newbler 2.8 software (roche), and gaps were closed by local assembly of selected reads in staden software [] into a single circular contig., the ncbi prokaryotic genome annotation pipeline [] was used for automated genome annotation, and functional annotations were carried […]

2017
PMCID: 5268455
PMID: 28125640
DOI: 10.1371/journal.pone.0170655

[…] in order to test the ability of rad-seq markers to capture undisclosed genetic diversity. the products of sanger sequencing were run on the 96-capillary 3730xl dna analyzer (applied biosystems®). staden package v2.0.0 [] was used to analyze dna sequences. the overall rate of fitted genotypes was estimated by dividing the total number of fitted genotypes with the total number of evaluated […]

2017
PMCID: 5346843
PMID: 28285591
DOI: 10.1186/s13071-017-2057-0

[…] biotec™ (pretoria, south africa) using the vector primers sp6 (5′-tta tac gac tca cta tag gg-3′) and t7 (5′-tat tta ggt gac act ata-3′)., the obtained sequences were assembled and edited using the gap4 program of the staden package (version 1.6.0 for windows) []. homologous sequence searches of databases were performed using the blastn package []. a multiple sequence alignment was performed […]

2017
PMCID: 5364215
PMID: 28336590
DOI: 10.1128/genomeA.00037-17

[…] the average coverage was 26.8-fold for 454 and 171.44-fold for illumina. some gaps were closed using pcr and sanger sequencing of the products. analysis of the obtained sequences was completed using gap4 (version 4.11) software of the staden package (, ). the final draft genome of s. sphaeroides (16 contigs) consists of a single chromosome of 4.98 mb with an overall g+c content of 47.21%. gene […]

2017
PMCID: 5368605
PMID: 28350004
DOI: 10.1038/srep45302

[…] gelred prior to sanger sequencing (macrogen inc., seoul, rep. of korea; biological resources facility, australian national university, canberra, australia). dna trace sequences were assembled using staden pregap 4 and gap 4. species identity was confirmed through blastn searches against the non-redundant dna database in genbank. estimates of haplotype (h) and nucleotide (π) diversity […]


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Staden in publications

 (167)
PMCID: 5870975
PMID: 29584761
DOI: 10.1371/journal.pone.0194672

[…] after purification with pcr purification kit (sangon biotech, shanghai, china), all pcr products were sequenced directly with a primer-walking strategy., contiguous sequences were assembled using staden package v1.7.0 []. pcgs and rrna genes were identified based on homologous regions of published pyraloidea mitogenomes using the clustal x in mega 5 []. the trnascan-se [] was used to predict […]

PMCID: 5823993
PMID: 29472322
DOI: 10.1128/genomeA.00010-18

[…] were end sequenced with an abi 3730xl dna sequencer (life technologies, darmstadt, germany), processed with phred, and assembled using phrap (http://www.phrap.org). sequence editing was done using gap4 as part of the staden software package (), and final gap closure was performed by pcr and primer walking using a bio-x-act kit (bioline, london, united kingdom)., the linear plasmid plma1 […]

PMCID: 5852556
PMID: 29364862
DOI: 10.3390/genes9020060

[…] confirm the pacbio assemblies. the sequence of the smallest plasmid was assembled with mira v4.0.2 [] using both pacbio and illumina reads. contigs were ordered and joined using abacas v1.3.1 [] and gap4 [] included in the staden package []. finally, circlator v1.0.0 [] was used to circularize sequences, to fix the origin of replication (dnaa in the chromosome and repa in plasmids), […]

PMCID: 5660504
PMID: 28835501
DOI: 10.1128/JVI.01137-17

[…] strains u1102, gs, and aj (, ) and alignment of the 21 cihhv-6b genomes with the two previously published hhv-6b genomes from the nonintegrated viruses hst and z29 (, ) were carried out using gap4 (). variation across the cihhv-6 genomes was studied by a combination of manual inspection and automated analysis using an in-house perl script. the script performed a sliding-window count […]

PMCID: 5569534
PMID: 28852435
DOI: 10.1186/s40793-017-0259-x

[…] products with bigdye 3.0 chemistry and an 10.1601/strainfinder?urlappend=%3fid%3dabi+3730xl capillary sequencer (applied biosystems, life technology gmbh, darmstadt, germany). manually editing in gap4 (version 4.11) software of the staden package [] was performed to improve the sequence quality. for final gap closure pacbio sequencing was used. a total of 27,870 pacbio reads with a mean […]


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Staden institution(s)
Laboratory of Molecular Biology, Hills Road, CB, Cambridge, UK

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