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Metassembler specifications


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


No version available


  • person_outline Michael Schatz <>

Publication for Metassembler

Metassembler citations


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

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

[…] 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 […]


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

PMCID: 5882950
PMID: 29615780
DOI: 10.1038/s41598-018-23749-w

[…] similar to the human genome but higher than both the fish and the bird. overall, these metrics suggest that the raw sequencing data was suitable for de novo assembly., de novo assembly using metassembler produced a genome of 159,132,706 bp (estimated percentage of genome assembled is 82%), with an average sequencing coverage of 66x (after adaptor trimming). the assembly is composed […]


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

PMCID: 5906920
PMID: 29684203
DOI: 10.1093/gbe/evy058

[…] last accessed december 13, 2017 (rrrkrtaytryqllelekefhfnryltrrrrielahslnlterhikiwfqnrrmkwkken)., contiguous sequences from both paedocypris genomes were extracted from the scaffolds assembled with metassembler, spanning all hit regions plus 10 kb upstream and downstream of each hit. these scaffold sequences were aligned to the orthologous sequences extracted from the zebrafish genome (grcz10) […]


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

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

[…] 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, […]


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

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

[…] and a published sultanina allpaths-lg assembly (ap). the strategies were: 1) a default platanus assembly (plat_d) for direct comparison with ap assembly, 2) an iterative merging strategy using metassembler to combine plat_d and ap assemblies (merge) and 3) platanus parameter modifications plus gapcloser (plat*_gc)., the three new assemblies were greater in size than the ap assembly. […]


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

PMCID: 5663730
PMID: 29163486
DOI: 10.3389/fimmu.2017.01407

[…] using multiple k-mers 55, 65, 75, 85, 95, 105, and 125, and the optimal assemblies were identified using assembly statistics generated by quastv2.3. the optimal assemblies were then combined using metassembler (), to obtain a single superior assembly., we ordered the assembled contigs against the complete ig loci of the african green monkey using mummerv3.23 (). the order was assigned based […]

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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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