CONTIGuator statistics

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Citations per year

Number of citations per year for the bioinformatics software tool CONTIGuator
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Tool usage distribution map

This map represents all the scientific publications referring to CONTIGuator per scientific context
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Associated diseases

This word cloud represents CONTIGuator usage per disease context
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Protocols

CONTIGuator specifications

Information


Unique identifier OMICS_06936
Name CONTIGuator
Software type Application/Script, Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 2.7
Stability Stable
Requirements
BioPython, Blast+, Perl (optional), ABACAS (optional), MUMmer (optional), Primer3
Maintained Yes

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Versioning


No version available

Documentation


Maintainers


  • person_outline Alessio Mengoni
  • person_outline Marco Galardini

Additional information


Web app: http://combo.dbe.unifi.it/contiguator

Information


Unique identifier OMICS_06936
Name CONTIGuator
Software type Application/Script, Package/Module
Interface Command line interface, Web user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python, Python
License BSD 3-clause “New” or “Revised” License
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainers


  • person_outline Alessio Mengoni
  • person_outline Marco Galardini

Additional information


Web app: http://combo.dbe.unifi.it/contiguator

Publication for CONTIGuator

CONTIGuator citations

 (99)
library_books

Genome comparison of different Zymomonas mobilis strains provides insights on conservation of the evolution

2018
PLoS One
PMCID: 5919020
PMID: 29694430
DOI: 10.1371/journal.pone.0195994

[…] software programs to assemble the genome of Z.mobilis, including Edena V3 [] and Velvet [].These scaffolds were ordered relative to the genome of the Z. mobilis strain ZM4, using a combination of the Contiguator [] and ACT 10.2.0 []. The Illumina reads were remapped to the scaffolds using Bowtie 0.12.7[] and visualized by Tablet 1.12.02.06[]. Annotation was primarily done by Prokka[], which uses P […]

library_books

Bordetella pseudohinzii targets cilia and impairs tracheal cilia driven transport in naturally acquired infection in mice

2018
Sci Rep
PMCID: 5890243
PMID: 29632402
DOI: 10.1038/s41598-018-23830-4

[…] 01 (LRUJ00000000), B. avium 197NT (NC_010645), B. holmesii ATCC 51541T (NZ_CP007494), B. pertussis Tohama IT (BX470248), B. petrii DSM 12804 (NC_010170) and B. trematum H044680328T (NZ_LT546645) with Contiguator. Subsequently, pseudo-genomes were annotated via Prokka.Sequencing reads were quality clipped as described before and mapped onto aforementioned Bordetella genomes with bowtie2. Afterwards […]

call_split

Draft Genome Sequence of Plant Growth Promoting and Drought Tolerant Bacillus altitudinis FD48, Isolated from Rice Phylloplane

2018
Genome Announc
PMCID: 5834328
PMID: 29496824
DOI: 10.1128/genomeA.00019-18
call_split See protocol

[…] done to qualify reads with a Phred score of >30 for downstream analysis. Reads that passed QC were subjected to de novo assembly using Velvet (version 1.2.10), followed by genome finishing using the CONTIGuator tool (, ), resulting in a genome size of 3.7 Mb with 15 scaffold sequences and 41.19% G+C content. The N50 contig size was 976,391 bp.A total of 4,029 predicted genes, including 3,964 prot […]

library_books

Tailed giant Tupanvirus possesses the most complete translational apparatus of the known virosphere

2018
Nat Commun
PMCID: 5829246
PMID: 29487281
DOI: 10.1038/s41467-018-03168-1

[…] lumina Inc., San Diego, CA, USA) with the paired end application. The sequence reads were assembled de novo using ABYSS software and SPADES, and the resulting contigs were ordered by the Python-based CONTIGuator.py software. The obtained draft genomes were mapped back to verify the read assembly and close gaps. The best assembled genome was retained, and the few remaining gaps (three) were closed […]

library_books

Pseudomonas rhizophila S211, a New Plant Growth Promoting Rhizobacterium with Potential in Pesticide Bioremediation

2018
Front Microbiol
PMCID: 5829100
PMID: 29527191
DOI: 10.3389/fmicb.2018.00034

[…] the A5-miseq pipeline, an integrated pipeline for de novo assembly of microbial genomes (Tritt et al., ), and finally analyzed with QUAST (Gurevich et al., ). These contigs were finally ordered using CONTIGuator v2.3 (Galardini et al., ) with its closely related genomes, P. lini (NZ_LT629746.1), P. frederiksbergensis (NZ_CP017886.1) P. mandelii JR-1 (NZ_CP005960.1), and P. brassicacearum (CP012680 […]

call_split

Complete Genome Sequence of Xanthomonas arboricola pv. juglandis Strain DW3F3, Isolated from a Juglans regia L. Bacterial Blighted Fruitlet

2018
Genome Announc
PMCID: 5824001
PMID: 29472324
DOI: 10.1128/genomeA.00023-18
call_split See protocol

[…] After sequencing, reads were assembled using the SPAdes software (), resulting in 8 contigs, with an N50 value of 1,706,766 bp and a smallest contig of 1,696 bp. These contigs were ordered using the CONTIGuator software () against many genomes of the same genus. The genome of X. campestris strain 17 (GenBank accession number CP011256) was used as a reference due to better synteny and number of co […]


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CONTIGuator institution(s)
Department of Evolutionary Biology, University of Firenze, Firenze, Italy; Interdisciplinary Research Institute USR3078 – CNRS University of Lille 1 - Université de Lille 2, Villenenuve d’Ascq, France

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