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NOVOPlasty specifications

Information


Unique identifier OMICS_13379
Name NOVOPlasty
Software type Package/Module
Interface Command line interface
Restrictions to use None
Output format FASTA, TXT
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Version 1.1
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Nicolas Dierckxsens

Publication for NOVOPlasty

NOVOPlasty citations

 (5)
call_split

The chloroplast genome of Cerasus humilis: Genomic characterization and phylogenetic analysis

2018
PLoS One
PMCID: 5919044
PMID: 29694421
DOI: 10.1371/journal.pone.0196473
call_split See protocol

[…] removed, thereby resulting in 20.86 Gb of clean data, with a quality value ≥ Q30, accounting for 91.37%. The genome of P. pseudocerasus was used as reference (GenBank Accession No. NC_030599.1), and NOVOPlasty software was used to assemble the chloroplast genome, the mistake parameter was set by default []. Three software were used for genome degenerate base correction, namely, bwa, samtools, and […]

library_books

Practical considerations for plant phylogenomics

2018
Appl Plant Sci
PMCID: 5895195
PMID: 29732268
DOI: 10.1002/aps3.1038

[…] te. Acquiring full chloroplast genomes for each sample can add extra time to data generation and analysis; however, multiple assembly pipelines (e.g., ACRE [Wysocki et al., ], IOGA [Bakker et al., ], NOVOPlasty [Dierckxsens et al., ], Fast‐Plast [https://github.com/mrmckain/Fast-Plast], and a k‐mer‐based approach [Izan et al., ]) have been developed that are capable of assembling complete chloropl […]

call_split

Complete Chloroplast Genome Sequence of Cane Needle Grass, Nassella hyalina (Poaceae: Stipeae)

2017
Genome Announc
PMCID: 5701466
PMID: 29167241
DOI: 10.1128/genomeA.01215-17
call_split See protocol

[…] lity control (QC) requirements were used for library construction (500-bp insert size) before being sequenced on an Illumina HiSeq 2000 sequencer to generate 125-bp paired-end reads (BGI, Hong Kong). NOVOPlasty (), an algorithm specifically developed for the de novo assembly of mitochondrial and chloroplast genomes from whole-genome data, was applied to extract chloroplast genome sequences from th […]

call_split

Mitochondrial genomes of the key zooplankton copepods Arctic Calanus glacialis and North Atlantic Calanus finmarchicus with the longest crustacean non coding regions

2017
Sci Rep
PMCID: 5651803
PMID: 29057900
DOI: 10.1038/s41598-017-13807-0
call_split See protocol

[…] performed using estwise algorithm implemented in wise2 software, using hmm profiles of all mitochondrial protein coding sequences (CDS). Identified transcripts were then used as baits in MITObim and NOVOPlasty assemblers to retrieve the mitogenomes from the sets of NGS sequencing reads.Gene annotations have been done semi-automatically. De novo prediction of all protein-coding genes was attempted […]

call_split

Sequencing and De Novo Assembly of the Complete Chloroplast Genome of the Peruvian Carrot (Arracacia xanthorrhiza Bancroft)

2017
Genome Announc
PMCID: 5313604
PMID: 28209812
DOI: 10.1128/genomeA.01519-16
call_split See protocol

[…] ojects/trim_galore/). The resulting 7.9 million sequencing reads generated an estimated 1,101-fold chloroplast genome coverage. The de novo assembly of the filtered pair-end reads was performed using NOVOPlasty (). Two annotation tools, CPGAVAS () and DOGMA (), were used to annotate the cp genome. Finally, protein-coding genes were manually annotated.The current investigation suggests that the A.  […]

Citations

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NOVOPlasty institution(s)
Interuniversity Institute of Bioinformatics in Brussels, Vrije Universiteit Brussel, Brussels, Belgium; Evolutionary Biology and Ecology Unit, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium; Genetics, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels, Belgium; Center for Medical Genetics, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
NOVOPlasty funding source(s)
This project was supported through a ULB-VUB PhD seed funding given to the Interuniversity Institute of Bioinformatics in Brussels and a PhD bursary of the Belgian Kids Fund. It was also funded by Funding Hopital Universitaire des Enfants Reine Fabiola through a support from the Fonds iris-Recherche.

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