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Citations per year

Number of citations per year for the bioinformatics software tool MaxBin
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Tool usage distribution map

This map represents all the scientific publications referring to MaxBin per scientific context
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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

 (44)
library_books

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

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

[…] ssembly 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. In part […]

library_books

Microbiome Dynamics in a Large Artificial Seawater Aquarium

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

[…] n 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, includin […]

library_books

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

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

[…] e 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 (, ) and reassemble […]

library_books

Studying microbial functionality within the gut ecosystem by systems biology

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

[…] ad 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, such as […]

library_books

Physiological and Metagenomic Characterizations of the Synergistic Relationships between Ammonia and Nitrite Oxidizing Bacteria in Freshwater Nitrification

2018
Front Microbiol
PMCID: 5835065
PMID: 29535685
DOI: 10.3389/fmicb.2018.00280

[…] in the genomes (0–2.4%, Supplementary Table ) suggest a high quality for the resulting bins. Furthermore, the high similarity of the bins (72.7–100%) obtained using two different binning approaches (MaxBin and differential coverage binning, Supplementary Table ) indicates the reliability of the binning results.Phylogenetic analysis using PhyloPhlAn based on whole genomes shows that the two AOB dr […]

call_split

Draft Genome Sequence of a Novel Thermofilum sp. Strain from a New Zealand Hot Spring Enrichment Culture

2018
Genome Announc
PMCID: 5823990
PMID: 29472320
DOI: 10.1128/genomeA.00005-18
call_split See protocol

[…] ng an Illumina MiSeq instrument. Adaptors and low-quality reads were removed using Trimmomatic () and assembled using IDBA-UD (). Contigs of less than 1 kb were removed. The contigs were binned using MaxBin (), resulting in the nearly complete genome of Thermofilum sp. strain NZ13. Three additional bins for a Fervidicoccus sp., a Desulfurococcaceae sp., and a Pyrobaculum sp. were also generated. O […]


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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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