Protocols

ploidyNGS specifications

Information


Unique identifier OMICS_14078
Name ploidyNGS
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Sequenced genome
Input format BAM
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python, R
License GNU General Public License version 3.0
Computer skills Advanced
Version 3.1.2
Stability Stable
Requirements
ggplot2, numpy, pysam, virtualenv, python 2.7.8, biopython 1.66, ploidyngs
Maintained Yes

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Versioning


No version available

Documentation


Maintainer


  • person_outline Diego Riano

Publication for ploidyNGS

ploidyNGS citation

call_split

Draft Genome Sequence of Saccharomyces cerevisiae Barra Grande (BG 1), a Brazilian Industrial Bioethanol Producing Strain

2017
Genome Announc
PMCID: 5374244
PMID: 28360170
DOI: 10.1128/genomeA.00111-17
call_split See protocol

[…] e mate-pair reads) (), and Trimmomatic () tools. Genome assembly was carried out with SPAdes version 3.7.1 (), Pilon version 1.16 (), and Redundans (). Assessment of ploidy level was carried out with ploidyNGS (). BG-1 is a diploid organism. The haploid nuclear genome is assembled in 215 scaffolds, and additional scaffold contains the full 2-µm plasmid sequence. The nuclear genome has a total leng […]

ploidyNGS institution(s)
Laboratorio Nacional de Ciencia e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Sao Paulo, Brazil; Faculdade de Ciencias Farmaceuticas de Ribeirao Preto, Universidade de Sao Paulo, Ribeirao Preto, Brazil; Laboratorio Nacional de Ciencia e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Sao Paulo, Brazil
ploidyNGS funding source(s)
Supported by the Sao Paulo State Research Foundation-FAPESP (2014/15799-7).

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