MeDuSa protocols

MeDuSa specifications

Information


Unique identifier OMICS_07882
Name MeDuSa
Alternative name Multi-Draft based Scaffolder
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 1.3
Stability Stable
Maintained Yes

Versioning


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Maintainer


  • person_outline Marco Fondi <>

Information


Unique identifier OMICS_07882
Name MeDuSa
Alternative name Multi-Draft based Scaffolder
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 1.3
Stability Stable
Maintained Yes

Maintainer


  • person_outline Marco Fondi <>

Publication for Multi-Draft based Scaffolder

MeDuSa IN pipelines

 (4)
2017
PMCID: 5477393
PMID: 28546480
DOI: 10.1128/genomeA.00371-17

[…] the reads were first assembled using spades 3.9 (77 k-mer, single-cell mode, >1,000-bp length) as recommended for high-gc data sets (3). this was used to obtain an 81-gapped contig scaffold using medusa (4), a multidraft-based analysis using 3 related species, streptomyces griseus, streptomyces scabiei and streptomyces hygroscopicus, with full-genome sequences. the total number of contigs […]

2017
PMCID: 5499129
PMID: 28584079
DOI: 10.1534/g3.117.040022

[…] equal to or larger than this value. the initial assembly is after hierarchical genome assembly process pipeline assembly of raw reads. the current assembly has undergone scaffolding with medusa and removal of scaffolding errors., to analyze the divergence of w303 from its parent strain, s288c, the genomes were aligned using mauve (darling et al. 2010). figure 1 shows the collinear […]

2017
PMCID: 5658503
PMID: 29074665
DOI: 10.1128/genomeA.01188-17

[…] contigs were then subjected to scaffolding and anchoring against the nearest reference genome of r. solani ag1-1a (genbank assembly accession number gca_000334115.1) to generate a draft genome using medusa (11). scaffolds with lengths shorter than 500 bp were excluded to reduce the fragmented nature of the assembly., the final draft of 28,929,909 bp was generated and assembled into 1,517 […]

2017
PMCID: 5666144
PMID: 28916559
DOI: 10.1128/AEM.01578-17

[…] performed at the joint genome institute (jgi; walnut creek, ca, usa). the illumina and 454 reads were combined into a single assembly using the newbler runassembly command (45) and scaffolded using medusa (46) based on the consensus order and orientation of t. reesei version 2, t. atroviride version 2, and t. virens version 2 genomes downloaded from jgi. data are available under ncbi bioproject […]

MeDuSa institution(s)
ComBo, Florence Computational Biology group, Dep of Biology, University of Florence, Sesto Fno, Italy

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