Chromaseq specifications

Information


Unique identifier OMICS_01017
Name Chromaseq
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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Chromaseq in publications

 (16)
PMCID: 5846723
PMID: 29529094
DOI: 10.1371/journal.pone.0192502

[…] with exo-sap-it (thermo fisher scientific, waltham ma, usa) according to manufacturer's instructions and sanger sequencing performed by the uc davis ucdna sequencing facility (davis, ca, usa). chromaseq was used to call bases and assemble contigs [–]; sequences were uploaded to genbank ()., initial determinations of the downy mildew samples were based on host and sporangial morphology […]

PMCID: 5707830
PMID: 29214050
DOI: 10.1186/s40851-017-0084-5

[…] 0 °c were performed. amplified dna fragments were purified with isopropanol, and then formamide was added. sequences were determined on an abi 3730 dna analyzer, assembled and edited with phred/phrap/chromaseq [–], and aligned by using muscle [] in mega7 []., nine y-linked microsatellite alleles (y318.1, y318.2, y318.4, y318.6, y318.9, y369.1, y369.4, y69217.1, and y15020.1) were determined by usi […]

PMCID: 5672585
PMID: 29118594
DOI: 10.3897/zookeys.688.13575

[…] automatic sequencer. assembly of multiple chromatograms of each gene fragment and initial base calls were made with phred v. 0.020425.c () and phrap v. 0.990319 () as orchestrated by mesquite’s chromaseq v. 1.12 package (, ) with subsequent modifications by chromaseq and manual inspection. final sequences are available on genbank (accessions mf370333‒mf370336)., sequences were incorporated […]

PMCID: 5361657
PMID: 28382021
DOI: 10.3389/fmicb.2017.00350

[…] foster city, ca, usa) using pcr primers (5 μm) at the university of arizona genomics core., an assembly pipeline consisting of phred and phrap (ewing and green, ; ewing et al., ) driven by chromaseq (maddison and maddison, ) in mesquite v.2.75 (maddison and maddison, ) was used to call bases and assemble bidirectional reads into contigs. base calls were verified by manual inspection […]

PMCID: 5215913
PMID: 28056072
DOI: 10.1371/journal.pone.0169637

[…] were purified using the axyprep pcr clean-up kit (axigen biosciences, ca, usa) and sequenced on both strands by a commercial supplier. chromatograms were evaluated with mesquite software using the chromaseq package [–], with phred and phrap algorithms for base calling, assigning quality values to each one and assembling contigs [–]., all sequences were subjected to blast search in the genbank […]


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