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Protocols

MaxBin specifications

Information


Unique identifier OMICS_10414
Name MaxBin
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
License BSD 2-clause “Simplified” License
Computer skills Advanced
Version 2.1.1
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Yu-Wei Wu <>

Publications for MaxBin

MaxBin citations

 (49)
library_books

An epizootic of Chlamydia psittaci equine reproductive loss associated with suspected spillover from native Australian parrots

2018
PMCID: 5953950
PMID: 29765033
DOI: 10.1038/s41426-018-0089-y

[…] v2 chemistry on an illumina miseq at the university of technology sydney. de novo genome assembly was carried out using spades v3.9 using the—careful flag to reduce potential misassembly events. maxbin v2.2.1 was used to cluster contigs according to abundance and gc content, thereby separating chlamydial and non-chlamydial contigs. finally, checkm v1.0.6 was used to assess the quality […]

library_books

Identifying Group Specific Sequences for Microbial Communities Using Long k mer Sequence Signatures

2018
PMCID: 5943621
PMID: 29774017
DOI: 10.3389/fmicb.2018.00872

[…] and clustering in microbial community studies., besides genes or species, assembled contigs have also been used as features to predict disease. several contig binning tools, such as concoct (), maxbin2.0 (), cocacola (), and metagen (), were developed for binning contigs assuming that contigs with similar coverage/relative abundances over different samples come from the same genomes. […]

library_books

Microbiome Dynamics in a Large Artificial Seawater Aquarium

2018
PMCID: 5930379
PMID: 29523545
DOI: 10.1128/AEM.00179-18

[…] in table s4. genomic bins, referred to here as metagenome-assembled genomes (mags), were then generated by using the reads from each sample and the coassembled metagenome (2,500-bp assembly), using maxbin 2.0 (). the recruitment of short reads to each mag was calculated by using bowtie2. metagenomes were imported into anvi'o v2.4.0 () for alignment, visualization, and manual refinement, […]

library_books

A genetically and functionally diverse group of non diazotrophic Bradyrhizobium spp. colonizes the root endophytic compartment of Arabidopsis thaliana

2018
PMCID: 5896095
PMID: 29642886
DOI: 10.1186/s12870-018-1272-y

[…] were removed from the genomes. assembly statistics were evaluated with quast v. 4.5 []. the gc content of the contigs revealed contamination in mos001 and mos004. the contamination was removed with maxbin v. 2.2.4 []. the orfs and proteome of the mossel assemblies were predicted with prodigal v. 2.6.1 []. assemblies were annotated with the prokka v1.11 tool []. a local blast database was made […]

library_books

Draft Genome Sequence of a Dictyoglomus sp. from an Enrichment Culture of a New Zealand Geothermal Spring

2018
PMCID: 5854780
PMID: 29545298
DOI: 10.1128/genomeA.00150-18

[…] sequenced on the illumina miseq platform. adapters and low-quality reads were trimmed using trimmomatic (), reads were assembled with idba-ud version 1.1.0 (, ), and contigs ≥1 kb were binned using maxbin version 1.4.5 (). to optimize the assembly, the reads were mapped back to the dictyoglomus sp. nz13-re01 draft genome using bowtie2 version 2.2.5 () and samtools version 1.2 (, ) […]

library_books

Studying microbial functionality within the gut ecosystem by systems biology

2018
PMCID: 5840735
PMID: 29556373
DOI: 10.1186/s12263-018-0594-6

[…] to closed genomes. the next challenge is therefore to determine which of the assembled contigs/scaffolds belong to a single species. this process has been termed binning, and several tools such as maxbin [] or metacluster [] have been developed to determine the amount of bins required and to assign contigs to bins. to do so, these tools take different types of information into account, […]


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MaxBin institution(s)
Joint BioEnergy Institute, Emeryville, CA, USA
MaxBin funding source(s)
This work was performed as part of the DOE Joint BioEnergy Institute supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, through contract DE-AC02-05CH11231 between Lawrence Berkeley National Laboratory and the U.S. Department of Energy.

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