Mugsy protocols

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Mugsy specifications

Information


Unique identifier OMICS_03606
Name Mugsy
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Mugsy accepts draft genomes in the form of multi-FASTA files and does not require a reference genome.
Input format FASTA
Operating system Unix/Linux
Computer skills Advanced
Version 1.2.3
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Samuel V. Angiuoli <>

Publication for Mugsy

Mugsy in pipelines

 (12)
2018
PMCID: 5872123
PMID: 29438308
DOI: 10.3390/antibiotics7010012

[…] center (brc). quality control and assembly was performed with the a5 pipeline [], and genomes were annotated using the online rast server []. multiple whole genome alignments were obtained with mugsy [], and trimal v1.2 removed poorly aligned regions []. orthologous genes were identified using itep [] with mcl clustering parameters as follows: inflation value = 2.0, cutoff = 0.04, maxbit […]

2018
PMCID: 5891936
PMID: 29643938
DOI: 10.1186/s13099-018-0242-0

[…] lead to mis-assembly. the lack of collinearity between the reference genome and these new assemblies also impaired the ability to align them for base-level comparisons. alignment programs like mugsy and mauve [] allow artificial re-arrangements of sequences to create locally collinear blocks (lcbs) for alignment. in our reference-guided approach, we added a manual curation step […]

2017
PMCID: 5241972
PMID: 28100185
DOI: 10.1186/s12864-016-3448-x

[…] second pass through the alignment blocks of the first assembly tried to connect scaffolds from the first assembly (ca454ilm) using scaffolds from other assemblies spanning two scaffolds in ca454ilm. mugsy was run with these options:, , we mapped all paired illumina and 454 reads to the assembly with bwa-mem 0.7.9a, and used the scaffold module from sga [] to scaffold the merged assembly, […]

2017
PMCID: 5607484
PMID: 28943892
DOI: 10.1186/s13099-017-0204-y

[…] sequence alignments were obtained from whole-genome sequences of 24 e. coli strains and from seven mlst genes of the e. coli isolates, i.e. adk, fumc, gyrb, icd, mdh, pura, and reca [, ], using mugsy (version 1.2.3) []. approximate maximum-likelihood phylogenetic trees were generated using fasttree (version 2.1.7) [] with the generalized time-reversible + cat model []. the resulting trees […]

2017
PMCID: 5624767
PMID: 28963221
DOI: 10.1128/genomeA.01058-17

[…] singletons, with a total number of bases in all reads of 239,929,351. the reads were assembled using abyss 2.0.2 (), spades 3.9.0 (), and ray 2.3.1 (), and consensus polishing was performed using mugsy 1.2.3 (). the assembly yielded 60 contigs of 201 to 520,919 bp in length, with a total length of 3,836,576 bp at 62× coverage and with an n50 value of 285,212 bp. the average genomic g+c […]


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Mugsy in publications

 (74)
PMCID: 5870499
PMID: 29580205
DOI: 10.1186/s12864-018-4597-x

[…] maximum likelihood trees were inferred with raxml []. determination of percent identity between chromosomes was determined through reference-independent whole-chromosome alignments using mugsy [] as described in reference []., we identified 450 single-copy orthologues on the main chromosome (list available from author wgq) using homolog identification by pairwise blastp and homolog […]

PMCID: 5859498
PMID: 29554870
DOI: 10.1186/s12864-018-4604-2

[…] de novo assembled using spades v3.7 and mapped to reference genomes nc_000898 and nc_001664 using bowtie2 [–]. contigs were aligned to reference genomes using the multiple alignment program mugsy v1.2.3 and resolved against consensus sequences from mapped reads using custom scripts in r/bioconductor [–]. final assemblies were generated after discarding any contigs with mapq <= 5. […]

PMCID: 5872123
PMID: 29438308
DOI: 10.3390/antibiotics7010012

[…] center (brc). quality control and assembly was performed with the a5 pipeline [], and genomes were annotated using the online rast server []. multiple whole genome alignments were obtained with mugsy [], and trimal v1.2 removed poorly aligned regions []. orthologous genes were identified using itep [] with mcl clustering parameters as follows: inflation value = 2.0, cutoff = 0.04, maxbit […]

PMCID: 5772174
PMID: 29249661
DOI: 10.1016/j.cub.2017.11.027

[…] using the previously annotated snps for the 32 strains, we reconstructed the sequence of each strain by replacing the reference nucleotide for a given snp. then, these 34 genomes were aligned using mugsy v1.2.3 []. the resulting alignment was trimmed using trimal v.1.4 []þto delete positions with more than 50% gaps. finally, a phylogenetic tree was reconstructed from the trimmed alignment using […]

PMCID: 5705806
PMID: 29202045
DOI: 10.1128/mSphere.00511-17

[…] p value for multiple comparisons using the bonferroni method., when short-read data for reference guided mapping were unavailable, whole-genome alignment of genomes to atcc 15305 was performed using mugsy v 2.3 (). repetitive regions in the reference genome that were greater than 100 bp in size were identified using nucmer, and these regions were masked in the alignment used in downstream […]


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Mugsy institution(s)
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA; Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA

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