Tag: Binning

MetaCluster 5.0.1 / MetaCluster-TA 1.2.1 / MetaAnnotator 1.4.4beta – Binning and Annotation Tool for Metagenomic Sequences

MetaCluster 5.0.1 / MetaCluster-TA 1.2.1 / MetaAnnotator1.4.4beta

:: DESCRIPTION

MetaCluster is an unsupervised binning method for metagenomic sequences.Existing binning methods based on sequence similarity and sequence composition markers rely heavily on the reference genomes of known microorganisms and phylogenetic markers. While MetaCluster is an integrated binning method based on the unsupervised top-down separation and bottom-up merging strategy, it can bin metagenomic sequencing datasets with mixed complex species abundance ratios from the exactly equal situation to the extremely unbalanced situation with consistently higher accuracy when compared with other recently reported methods.

MetaCluster-TA is a new software for binning and annotating short paired-end reads.

MetaAnnotator is a novel software for binning and annotating short paired-end reads.

::DEVELOPER

Bioinformatics Research Group of Hong Kong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MetaCluster , MetaCluster-TA , MetaAnnotator

:: MORE INFORMATION

Citation:

BMC Genomics. 2014;15 Suppl 1:S12. doi: 10.1186/1471-2164-15-S1-S12. Epub 2014 Jan 24.
MetaCluster-TA: taxonomic annotation for metagenomic data based on assembly-assisted binning.
Wang Y, Leung H, Yiu S, Chin F.

Wang, Yi, Henry C.M. Leung, S.M. Yiu, Francis Y.L. Chin. (2012)
MetaCluster 4.0: A Novel Binning Algorithm for NGS Reads and Huge Number of Species,
Journal of Computational Biology, 19, 241-249.

MsatAllele 1.05 – Visualize the Binning of Microsatellite Alleles

MsatAllele 1.05

:: DESCRIPTION

MsatAllele is a computer package built on R to visualize and bin the raw microsatellite allele size distributions.

::DEVELOPER

Filipe Alberto’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • R

:: DOWNLOAD

 MsatAllele

:: MORE INFORMATION

Citation

J Hered. 2009 May-Jun;100(3):394-7. doi: 10.1093/jhered/esn110. Epub 2009 Jan 6.
MsatAllele_1.0: An R package to visualize the binning of microsatellite alleles.
Alberto F.

d2SBin v1.0 – Improving the Binning of Metagenomic Contigs on d2S Oligonucleotide Frequency Dissimilarity

d2SBin v1.0

:: DESCRIPTION

d2SBin is easy-to-use contig-binning improving tool, which adjusted the contigs among bins based on the output of any existing binning tools. The tool is taxonomy-free only on the k-tuples for single metagenomic sample.

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux
  • Python

:: DOWNLOAD

d2SBin

:: MORE INFORMATION

Citation

Wang Y, Wang K, Lu YY, Sun F.
Improving contig binning of metagenomic data using [Formula: see text] oligonucleotide frequency dissimilarity.
BMC Bioinformatics. 2017 Sep 20;18(1):425. doi: 10.1186/s12859-017-1835-1. PMID: 28931373; PMCID: PMC5607646.

Tandem2 – Automated Microsatellite Allele Binning for Population Genetics Workflows

Tandem2

:: DESCRIPTION

All microsatellite analysis software expects allele sizes given in integer numbers, while allele scoring produces allele sizes with two decimals that are dependent not only on fragment length, but also on fluorescent dye, and GC content. Therefore, allele binning is not a trivial task. Tandem2 fills a gap of the microsatellite workflow by rounding allele sizes to valid integers, depending on the microsatellite repeat units.

::DEVELOPER

EVOINFORMATICS GROUP

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • MacOsX

:: DOWNLOAD

 Tandem2

:: MORE INFORMATION

Citation

Matschiner M, Salzburger W (2009)
TANDEM: integrating automated allele binning into genetics and genomics workflows.
Bioinformatics, 25(15), 1982-1983.

flowBin 1.28.0 – Combining Multitube Flow Cytometry data by Binning

flowBin 1.28.0

:: DESCRIPTION

flowBin is a parameterisation-free method for combining multitube flow cytometry data into a higher-dimensional form suitable for deep profiling and discovery.

::DEVELOPER

Kieran O’Neill <koneill at bccrc.ca>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux /MacOs
  • R
  • Bioconductor

:: DOWNLOAD

 flowBin

:: MORE INFORMATION

Citation

Deep profiling of multitube flow cytometry data.
O’Neill K, Aghaeepour N, Parker J, Hogge D, Karsan A, Dalal B, Brinkman RR.
Bioinformatics. 2015 Jan 18. pii: btv008.

MaxBin 2.2.7 – Binning Assembled Metagenomic Sequences

MaxBin 2.2.7

:: DESCRIPTION

MaxBin is a software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.

::DEVELOPER

The Joint BioEnergy Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MaxBin

:: MORE INFORMATION

Citation

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets.
Wu YW, Simmons BA, Singer SW.
Bioinformatics. 2015 Oct 29. pii: btv638.

MetaProb v2 – Accurate Metagenomic Reads Binning based on Probabilistic Sequence Signatures

MetaProb v2

:: DESCRIPTION

MetaProb is a novel assembly-assisted tool for unsupervised metagenomic binning.

::DEVELOPER

Matteo Comin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

MetaProb 

:: MORE INFORMATION

Citation

Bioinformatics, 32 (17), i567-i575 2016 Sep 1
MetaProb: Accurate Metagenomic Reads Binning Based on Probabilistic Sequence Signatures
Samuele Girotto 1, Cinzia Pizzi 1, Matteo Comin 1

MBBC 1.1 – Metagenomic Binning Based on Composition

MBBC 1.1

:: DESCRIPTION

MBBC is a useful tool in metagenomic studies. It is a novel composition-based approach to bin environmental shotgun reads, by considering the k-mer frequency in reads and the inferred Markovian property of the unknown species or OTUs (operational taxonomic units).

::DEVELOPER

Hu Lab – Data Integration and Knowledge Discovery @ UCF

:: SCREENSHOTS

MBBC

:: REQUIREMENTS

  • Linux / WIndows/ MacOsX
  • Java

:: DOWNLOAD

 MBBC

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2015 Feb 5;16(1):36. [Epub ahead of print]
MBBC: an efficient approach for metagenomic binning based on clustering.
Wang Y, Hu H, Li X.

AbundanceBin 1.0.1 – Abundance-based tool for Binning Metagenomic Sequences

AbundanceBin 1.0.1

:: DESCRIPTION

AbundanceBin is an abundance-based tool for binning metagenomic sequences, such that the reads classified in a bin belong to species of identical or very similar abundances. AbundanceBin also gives estimations of species abundances and their genome sizes—-two important characteristic parameters for a microbial community.

::DEVELOPER

Yuzhen Ye lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 AbundanceBin

:: MORE INFORMATION

Citation:

Yu-Wei Wu and Yuzhen Ye.
A novel abundance-based algorithm for binning metagenomic sequences using l-tuples.
Lecture Notes in Computer Science2010, Volume 6044/2010, 535-549 (RECOMB 2010)

DynBin – Binning Microbial Community Profiles

DynBin

:: DESCRIPTION

DynBin is a dynamic programming algorithm based binning method for ARISA data analysis which minimizes the overall differences between replicates from the same sampling spot. Data preprocessing identifies several outliers which are later found to be due to systematic errors. Clustering analysis of the time spots based on the binned data reveals important features of the biodiversity of the microbial communities.

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 DynBin

:: MORE INFORMATION

Citation

Quansong Ruan, Joshua A. Steele, Michael S. Schwalbach, Jed A. Fuhrman, Fengzhu Sun (2006),
A Dynamic Programming Algorithm for Binning Microbial Community Profiles.
Bioinformatics 22:1508-1514