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Magnolya specifications


Unique identifier OMICS_00347
Name Magnolya
Alternative name matched genomes de novo assembly graph analysis
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTA
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 0.15
Stability Stable
Maintained Yes




No version available



  • person_outline Dick de Ridder

Publication for matched genomes de novo assembly graph analysis

Magnolya citations


Evolutionary Engineering in Chemostat Cultures for Improved Maltotriose Fermentation Kinetics in Saccharomyces pastorianus Lager Brewing Yeast

Front Microbiol
PMCID: 5596070
PMID: 28943864
DOI: 10.3389/fmicb.2017.01690
call_split See protocol

[…] umina HiSeq2500 sequencer (Illumina). A total of 4.3 Gb and 4.6 Gb of 150-bp paired-end fragments were generated for IMS0493 and CBS1483 respectively. Chromosome copy numbers were estimated using the Magnolya software tool (Nijkamp et al., ; Oud et al., ). For visualization purposes, assembled contigs and their copy number were mapped on an illumina reads based-assembly of S. pastorianus CBS1483 ( […]


The adaptive landscape of wildtype and glycosylation deficient populations of the industrial yeast Pichia pastoris

BMC Genomics
PMCID: 5553748
PMID: 28797224
DOI: 10.1186/s12864-017-3952-7
call_split See protocol

[…] esults. SNP/indel locations called from reads of the assembly strain were considered as false-positive and removed. The remaining hits were manually reviewed with a genome browser.With cn.mops [] and Magnolya [] two different approaches to detect potential copy number variations (CNVs) were applied. cn.mops was chosen due to its applicability for haploid organisms. Magnolya, which uses co-assembli […]


Implications of evolutionary engineering for growth and recombinant protein production in methanol based growth media in the yeast Pichia pastoris

Microb Cell Fact
PMCID: 5356285
PMID: 28302114
DOI: 10.1186/s12934-017-0661-5
call_split See protocol

[…] stus [] was used for gene prediction. Annotation was performed by matching predicted genes against the CBS 7435 reference strain using blast. Variant-calling was performed using kSNP3 [] and GATK []; Magnolya [] and cn.mops [] were applied in order to test for potential CNVs in the evolved strains. Co-assembly for Magnolya was performed with velvet []. Alignment files were manually reviewed using […]


A new laboratory evolution approach to select for constitutive acetic acid tolerance in Saccharomyces cerevisiae and identification of causal mutations

Biotechnol Biofuels
PMCID: 4983051
PMID: 27525042
DOI: 10.1186/s13068-016-0583-1
call_split See protocol

[…] g to the CEN.PK113-7D sequence annotation []. Raw sequencing data have been deposited as short-read archives (Bioproject: PRJNA313456/SRP070976, individual accession numbers in Additional file ). The Magnolya algorithm was used to analyse copy number variation using Newbler (454 Life Sciences, Branford, CT) for co-assembly of sequence reads of CEN.PK113-7D and the sample of interest []. Integer co […]


Chromosomal Copy Number Variation in Saccharomyces pastorianus Is Evidence for Extensive Genome Dynamics in Industrial Lager Brewing Strains

Appl Environ Microbiol
PMCID: 4542246
PMID: 26150454
DOI: 10.1128/AEM.01263-15
call_split See protocol

[…] Table S4 in the supplemental material) were annotated by use of the MAKER2 pipeline () (see Table S5 in the supplemental material).The chromosomal copy number variation was estimated by applying the Magnolya program (). When there was no prior knowledge of the ploidy, the gamma setting was set to none. Magnolya uses a Poisson mixture model to estimate the integer copy number of an assembled conti […]


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Magnolya institution(s)
The Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Delft, The Netherlands; Department of Biotechnology, Delft University of Technology, Delft, The Netherlands; Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands; Heineken Supply Chain, Global Research & Development, Zoeterwoude, The Netherlands; Netherlands Bioinformatics Centre, Nijmegen, The Netherlands
Magnolya funding source(s)
Supported by the Kluyver Centre for Genomics of Industrial Fermentation, and the Netherlands Genomics Initiative.

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