NOVOPlasty specifications


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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  • person_outline Nicolas Dierckxsens <>

Publication for NOVOPlasty

NOVOPlasty in publications

PMCID: 5932399
PMID: 29755486
DOI: 10.3389/fpls.2018.00486

[…] 0.4–0.6 gb per sample. we removed the adapter sequences using scythe () and trimmed reads to remove low quality bases by sickle (). to assemble the organelle genomes, we input the reads into novoplasty (). for the plastome, we used the woodwardia assembly (genbank accession: nc_028543) as the seed. for the mitogenome, we used the coding exon sequences from salvinia mitogenome (li et al., […]

PMCID: 5895195
PMID: 29732268
DOI: 10.1002/aps3.1038

[…] 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 [], and a k‐mer‐based approach [izan et al., ]) have been developed that are capable of assembling complete […]

PMCID: 5651803
PMID: 29057900
DOI: 10.1038/s41598-017-13807-0

[…] 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 […]

PMCID: 5313604
PMID: 28209812
DOI: 10.1128/genomeA.01519-16

[…] 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 […]

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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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