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Consed specifications


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


No version available


  • person_outline David Gordon <>

Publications for Consed

Consed citations


Genome Guided Analysis of Clostridium ultunense and Comparative Genomics Reveal Different Strategies for Acetate Oxidation and Energy Conservation in Syntrophic Acetate Oxidising Bacteria

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 […]


Genome Sequences of 19 Novel Erwinia amylovora Bacteriophages

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 […]


Complete Genome Sequences of Mycobacteriophages Clautastrophe, Kingsolomon, Krypton555, and Nicholas

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 […]


Complete Genome Sequences of Cluster A Mycobacteriophages BobSwaget, Fred313, KADY, Lokk, MyraDee, Stagni, and StepMih

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 (, glimmer (), genemark (), starterator, phamerator (), hhpred (), blastp […]


Whole Genome Sequence of Bacillus cereus AR156, a Potential Biocontrol Agent with High Soilborne Disease Biocontrol Efficacy and Plant Growth Promotion

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 […]


Shared features of cryptic plasmids from environmental and pathogenic Francisella species

PMCID: 5570271
PMID: 28837612
DOI: 10.1371/journal.pone.0183554

[…] computationally shredded and merged using parallel phrap, version sps-4.24 [, ]. the resulting assembly was brought to improved status through both manual and computational finishing efforts using consed [] and in-house scripts. assembled genome sequences were corrected by mapping illumina reads (300x) back to the final consensus sequences using burrows-wheeler alignment (bwa) [], samtools [] […]

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

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