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Protocols

Metassembler specifications

Information


Unique identifier OMICS_10069
Name Metassembler
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License BSD 2-clause “Simplified” License
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Michael Schatz

Publication for Metassembler

Metassembler citations

 (13)
library_books

Comparison of the Chinese bamboo partridge and red Junglefowl genome sequences highlights the importance of demography in genome evolution

2018
BMC Genomics
PMCID: 5941490
PMID: 29739321
DOI: 10.1186/s12864-018-4711-0

[…] MaSuRCA v2.3.2 [], which uses its own raw data quality control tools. For computational feasibility, the three assemblies used Kmer values of 63, 63, and 35 respectively, and we merged scaffolds with Metassembler v1.5 []. We estimated proportions of repetitive elements with RepeatMasker v4.0.5 using the “Aves” repeat library [].We annotated scaffolds with a length of 1 kb or greater using MAKER v2 […]

call_split

De novo draft assembly of the Botrylloides leachii genome provides further insight into tunicate evolution

2018
Sci Rep
PMCID: 5882950
PMID: 29615780
DOI: 10.1038/s41598-018-23749-w
call_split See protocol

[…] timated using three different metrics: the N50 length, the BUSCO core-genes completion and the number of genes predicted by Glimmer. Second, these drafts were combined by following each ranking using Metassembler, hence producing three new assemblies (limiting the maximum insert size at 15 kb). Third, the B. leachii transcriptome was aligned to each meta-assembly using STAR, and their alignment pe […]

library_books

The Most Developmentally Truncated Fishes Show Extensive Hox Gene Loss and Miniaturized Genomes

2018
Genome Biol Evol
PMCID: 5906920
PMID: 29684203
DOI: 10.1093/gbe/evy058

[…] sing two different assembly programs, the “Overlap-Layout-Consensus” based Celera Assembler () and the “de Bruijn graph” based DISCOVAR de novo (). These two initial assemblies were then merged using Metassembler software (), resulting in a reconsolidated single assembly with superior quality for each of the two Paedocypris species. The quality of the genome assemblies was assessed on the basis of […]

library_books

Analysis of Vibrio seventh pandemic island II and novel genomic islands in relation to attachment sequences among a wide variety of Vibrio cholerae strains

2018
PMCID: 5900727
PMID: 29315809
DOI: 10.1111/1348-0421.12570

[…] s in CLC Genomics Workbench 8.5.1, and Velvet version 1.2.09 , . The resulting contigs with short length <200 bp were filtered out with home customized‐script. The assemblies were further improved by Metassembler version 1.5 , and MeGAMerge‐1.0 . Mapping of the reads to the references using CLC Genomics Workbench is a second approach in addition to the de novo assemblies. Strains O395, N16961, and […]

library_books

Comparison of three assembly strategies for a heterozygous seedless grapevine genome assembly

2018
BMC Genomics
PMCID: 5773036
PMID: 29343235
DOI: 10.1186/s12864-018-4434-2

[…] ompare with ALLPATHS-LG assembly (AP) []. Development of less fragmented and increased scaffold sized assemblies was approached through two separate strategies: 1) An iterative merging strategy using METASSEMBLER to combine two assemblies from different assemblers (MERGE); 2) A PLAT*_GC assembly was developed by altering branch cutting and contig scaffolding steps. In the PLAT*_GC assembly, mergin […]

library_books

Structure and Diversity of the Rhesus Macaque Immunoglobulin Loci through Multiple De Novo Genome Assemblies

2017
Front Immunol
PMCID: 5663730
PMID: 29163486
DOI: 10.3389/fimmu.2017.01407

[…] MP dataset, to obtain 50,703,106 “baited-Ig” reads. The baited-Ig reads and contigs were used as inputs for genome assembly using SPAdesv3.0 (), and the optimal assemblies were further combined using Metassembler (), to obtain 3 and 8 contigs representing the rhesus macaque IGL and IGK locus, respectively.The eight assembled macaque IGK contigs were ordered against the African green monkey IGK loc […]

Citations

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Metassembler institution(s)
Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México

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