Consed protocols

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Consed specifications

Information


Unique identifier OMICS_00879
Name Consed
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages C++
Computer skills Medium
Version 29.0
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Consed

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Maintainer


  • person_outline David Gordon <>

Publications for Consed

Consed in pipelines

 (16)
2017
PMCID: 5578845
PMID: 28860247
DOI: 10.1128/genomeA.00886-17

[…] the sequenced dna, was found to be approximately 15.3-fold. primer walking and pcr-based techniques were applied to close the remaining gaps. all of the manual editing steps were performed using the consed software package (, ). prediction of the operons in the b. cereus ar156 chromosomes was performed with an algorithm that combines intergenic distance and phylogenetic information (), and trnas […]

2017
PMCID: 5658500
PMID: 29074662
DOI: 10.1128/genomeA.01182-17

[…] at 26 to 37°c. all seven phages are morphologically members of the family siphoviridae. the genomes were sequenced using the illumina miseq platform with 150-bp reads and assembled using newbler and consed, with at least 300-fold coverage (, ). the genomes were annotated using dna master (http://cobamide2.bio.pitt.edu), glimmer (), genemark (), starterator, phamerator (), hhpred (), blastp […]

2016
PMCID: 4807237
PMID: 27013048
DOI: 10.1128/genomeA.00168-16

[…] ~7.5 million 150-bp reads were generated using an illumina miseq and aligned to the existing assembly for a total average coverage of ~350×. where possible, contigs were joined manually using consed version 22 (), reducing the number of contigs to 37. these contigs were scaffolded using blast similarity to arthrobacter aurescens tc1 (), and contigs were then joined by performing pcr […]

2016
PMCID: 4909266
PMID: 27304881
DOI: 10.1371/journal.pone.0156838

[…] used with the appropriate reagents scaled up proportionally. phage dna was sequenced using 454 sequencing technology and sequencing reads were assembled using newbler 2.9 (454 life sciences, roche), consed [], and gepard []. phage genomes were screened for direct terminal repeats using pause (https://cpt.tamu.edu/computer-resources/pause) and were annotated using dna master [] and other programs […]

2016
PMCID: 5010888
PMID: 27516530
DOI: 10.1093/gbe/evw138

[…] reads obtained from sequencing with genome analyzer gaiix (illumina, san diego, usa) by fasteris (plan les ouates, switzerland) were then mapped to the final assembly with bwa () and visualized with consed (). homopolymer errors were corrected in the plasmid and the chromosome sequence after manual inspection of discrepancies covered by >2 reads with a phred base quality score of >10. […]


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Consed in publications

 (74)
PMCID: 5924567
PMID: 29690652
DOI: 10.3390/genes9040225

[…] of the selected assembly was performed using sspace [] and the removal of possible gaps present in scaffolds was performed using gapfiller []. homopolymer errors were corrected manually using consed []. the purity of the scaffolds was also checked against the genome of t. aegyptius dsm 12793. possible miss-assemblies were corrected manually using tablet, a graphical viewer […]

PMCID: 5690319
PMID: 29146842
DOI: 10.1128/genomeA.00931-17

[…] (454 life sciences, roche diagnostics) or illumina hiseq 2500 sequencing (illumina, 250-bp reads). contigs were assembled using newbler version 2.9 (roche diagnostics, branford, ct) and consed () for 454 pyrosequencing reads or geneious version r8 () for illumina reads. assembled genomes were annotated using dna master () and other programs as described previously (, )., the 19 […]

PMCID: 5679797
PMID: 29122864
DOI: 10.1128/genomeA.01129-17

[…] of the family siphoviridae. following the isolation of double-stranded dna, genomes were sequenced using the illumina miseq platform, and 150-base single-end reads were assembled using newbler and consed (); coverage exceeded 1,800-fold for all genomes, and all have defined genome termini with 10-base complementary 3′ single-strand dna extensions (right end, 5′-tcgatcagcc). genome annotations […]

PMCID: 5658500
PMID: 29074662
DOI: 10.1128/genomeA.01182-17

[…] at 26 to 37°c. all seven phages are morphologically members of the family siphoviridae. the genomes were sequenced using the illumina miseq platform with 150-bp reads and assembled using newbler and consed, with at least 300-fold coverage (, ). the genomes were annotated using dna master (http://cobamide2.bio.pitt.edu), glimmer (), genemark (), starterator, phamerator (), hhpred (), blastp […]

PMCID: 5578845
PMID: 28860247
DOI: 10.1128/genomeA.00886-17

[…] the sequenced dna, was found to be approximately 15.3-fold. primer walking and pcr-based techniques were applied to close the remaining gaps. all of the manual editing steps were performed using the consed software package (, ). prediction of the operons in the b. cereus ar156 chromosomes was performed with an algorithm that combines intergenic distance and phylogenetic information (), and trnas […]


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Consed institution(s)
Department of Molecular Biotechnology, University of Washington, Seattle, WA, USA

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