Metassembler protocols

View Metassembler computational protocol

Metassembler statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Assembly reconciliation chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

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


Add your version

Maintainer


  • person_outline Michael Schatz <>

Publication for Metassembler

Metassembler in pipelines

 (4)
2018
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 […]

2017
PMCID: 5436433
PMID: 28521789
DOI: 10.1186/s13059-017-1213-3

[…] which includes the assemblies of s. aureus and r. sphaeroides. other assembly reconciliation tools used the assemblathon dataset [], which was a similar assembly competition to gage. for instance, metassembler used both the assemblathon 1 and assemblathon 2 datasets., all assembly reconciliation tools were run with default parameters, and quast [] was used to gather extensive assembly […]

2017
PMCID: 5465620
PMID: 28596401
DOI: 10.1128/genomeA.00474-17

[…] configuration, achieving a genome coverage of 120-fold. assembly was performed with spades version 3.9.0 and idba_ud version 1.1.1 parallel, and the contigs obtained were merged and optimized using metassembler version 1.5 (). contigs were reordered using mauve version snapshot_2015_02_13 using the genome of p. chlororaphis 189 as a reference ()., the draft genome of p. chlororaphis strain atcc […]

2017
PMCID: 5604772
PMID: 28818899
DOI: 10.1128/genomeA.00792-17

[…] which resulted in a total of 3,891,197 reads for a depth coverage of 300×. genome assembly was performed using spades version 3.9.0 () and idba_ud version 1.1.1 (). then, sspace version 3.0 () and metassembler version 1.5 () were used for merging and scaffolding the obtained contigs. after genome assembly and scaffolding, 12 contigs were obtained. phylogenetic analysis of the 16s rrna […]


To access a full list of citations, you will need to upgrade to our premium service.

Metassembler in publications

 (13)
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 […]

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 […]

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) […]

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, […]

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. […]


To access a full list of publications, you will need to upgrade to our premium service.

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

Metassembler reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Metassembler