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.

BECAS – Biomedical Concept Annotation Tool, API and Widget

BECAS

:: DESCRIPTION

becas is a web application, API and widget for biomedical concept identification. It helps researchers, healthcare professionals and developers in the identification of over 1,200,000 biomedical concepts in text and PubMed abstracts.

::DEVELOPER

UA.PT Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux/ MacOsX
Python

:: DOWNLOAD

BECAS API

:: MORE INFORMATION

Citation

BeCAS: biomedical concept recognition services and visualization.
Nunes T, Campos D, Matos S, Oliveira JL.
Bioinformatics. 2013 Aug 1;29(15):1915-6. doi: 10.1093/bioinformatics/btt317

TREAT 1.0.1 – Targeted RE-sequencing Annotation Tool

TREAT 1.0.1

:: DESCRIPTION

TREAT ( Targeted RE-sequencing Annotation Tool) offers an comprehensive, open framework, end-to-end solution for analyzing and interpreting targeted re-sequencing data. TREAT encompasses sequence alignment, variant calling, variant annotation, variant filtering, and visualization in one comprehensive analytic workflow. The rich set of annotations provided by TREAT enables the filtering of detected variants based on their functional characteristics, and visualizations at the variant positions allow the investigators to closely examine the identified variants of interest

::DEVELOPER

Bioinformatics Program, Division of Biomedical Statistics and Informatics, Mayo Clinic Research

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

TREAT

:: MORE INFORMATION

Citation:

TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data.
Asmann YW, Middha S, Hossain A, Baheti S, Li Y, Chai HS, Sun Z, Duffy PH, Hadad AA, Nair A, Liu X, Zhang Y, Klee EW, Kalari KR, Kocher JP.
Bioinformatics. 2012 Jan 15;28(2):277-8. Epub 2011 Nov 15.