AbundanceBin protocols

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AbundanceBin specifications

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Unique identifier OMICS_01471
Name AbundanceBin
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for AbundanceBin

AbundanceBin in pipeline

2014
PMCID: 4206474
PMID: 25337710
DOI: 10.1371/journal.pone.0110943

[…] reads and 241,486,162 bases. the raw data was pre-filtered to remove most human reads (55% of the total reads) using bowtie 2 with default parameters. the reads were then split into two bins using abundancebin : (1) a bin containing abundant reads including those derived from “ca. m. girerdii”, and (2) a bin containing less abundant reads derived from the minor components of the vaginal […]


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AbundanceBin in publications

 (7)
PMCID: 5767322
PMID: 29375610
DOI: 10.3389/fpls.2017.02241

[…] unique taxon to each cluster through a set of references computed on known genomes. however, none of these approaches is able to estimate genomes relative abundance (gras) for microbial communities. abundancebin (wu and ye, ) uses the content of k-mers in the reads to estimate abundance of the genomes. the main assumption in this process is that reads are sampled from genomes following a poisson […]

PMCID: 5148923
PMID: 27980708
DOI: 10.1016/j.csbj.2016.11.005

[…] of a larger bin belonging to highly abundant species. this issue can be solved by use of abundance based binning methods, which can be further subdivided into methods for working with one sample (abundancebin , mbbc ), and methods working with series of metagenomic samples (canopy ). the key idea of the first group is that the distribution of sequenced reads follows the lander-waterman model, […]

PMCID: 4628670
PMID: 26557648
DOI: 10.1155/2015/197895

[…] usage [, ], which can be directly extracted from the nucleotide sequences. according to different signatures or observations, a number of composition-based methods are proposed as the binning tools. abundancebin [] utilizes the k-mer frequency to group reads, while toss [] is based on sufficiently long mers and integrates abundancebin into separating reads from species with different abundances. […]

PMCID: 4402587
PMID: 25859745
DOI: 10.1186/1471-2105-16-S5-S2

[…] with automatic feature weighting mechanism to cluster these reads represented by topic distributions., experiments show that the new method tm-mcluster outperforms major existing methods, including abundancebin, metacluster 3.0/5.0 and mcluster. this result indicates that the exploitation of topic modeling can effectively improve the binning performance of metagenomic reads., due […]

PMCID: 4348430
PMID: 25750697
DOI: 10.1016/j.csbj.2014.11.009

[…] are classified into discrete clusters commonly referred to as bins. binning algorithms have been specifically developed for metagenomic sequence read assembly; examples of these include meta-idba , abundancebin , metavelvet and metacluster , , . further binning strategies can then be employed to retrieve single genomes from the fragmented assembled contigs. one of the most widely used binning […]


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AbundanceBin institution(s)
School of Informatics and Computing, Indiana University, Bloomington, IN, USA

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