Tag: Taxonomic Profiling

MetaMeta 1.2.0 – Integrating Metagenome analysis tools to improve Taxonomic Profiling

MetaMeta 1.2.0

:: DESCRIPTION

MetaMeta is a pipeline to execute and integrate results from metagenome analysis tools. It provides an easy workflow to run multiple tools with multiple samples, producing a single enhanced output profile for each sample.

::DEVELOPER

Vitor C. Piro

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

MetaMeta

:: MORE INFORMATION

Citation

Piro VC, Matschkowski M, Renard BY.
MetaMeta: integrating metagenome analysis tools to improve taxonomic profiling.
Microbiome. 2017 Aug 14;5(1):101. doi: 10.1186/s40168-017-0318-y. PMID: 28807044; PMCID: PMC5557516.

MetaPhyler 1.25 – Taxonomic Profiling for Metagenomic Sequences

MetaPhyler 1.25

:: DESCRIPTION

MetaPhyler is a novel taxonomic classifier for metagenomic shotgun reads, which uses phylogenetic marker genes as a taxonomic reference. Our classifier, based on BLAST, uses different thresholds (automatically learned from the reference database) for each combination of taxonomic rank, reference gene, and sequence length. Our reference database includes marker genes from all complete genomes, several draft genomes and the NCBI nr protein database. Results on simulated metagenomic datasets demonstrate that MetaPhyler outperforms previous tools used in this context (CARMA, MEGAN and PhymmBL).

::DEVELOPER

Bo Liu 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MetaPhyler

:: MORE INFORMATION

Citation:

BMC Genomics. 2011;12 Suppl 2:S4. Epub 2011 Jul 27.
Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences.
Liu B, Gibbons T, Ghodsi M, Treangen T, Pop M.

MicrobeGPS 1.0.0 – The Explorative Taxonomic Profiling Tool for Metagenomic Data

MicrobeGPS 1.0.0

:: DESCRIPTION

MicrobeGPS is a bioinformatics tool for the analysis of metagenomic sequencing data. The goal is to profile the composition of metagenomic communities as accurately as possible and present the results to the user in a convenient manner.

::DEVELOPER

MicrobeGPS Team

:: SCREENSHOTS

MicrobeGPS

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 MicrobeGPS

:: MORE INFORMATION

Citation

Metagenomic profiling of known and unknown microbes with microbeGPS.
Lindner MS, Renard BY.
PLoS One. 2015 Feb 2;10(2):e0117711. doi: 10.1371/journal.pone.0117711.