Tag: Metagenome

ATLAS 2.6a2 – Analyzing your Metagenome data

ATLAS 2.6a2

:: DESCRIPTION

Metagenome-atlas is a easy-to-use metagenomic pipeline based on snakemake. It handles all steps from QC, Assembly, Binning, to Annotation.

::DEVELOPER

Prof Zdobnov Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

ATLAS

:: MORE INFORMATION

Citation

Kieser S, Brown J, Zdobnov EM, Trajkovski M, McCue LA.
ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data.
BMC Bioinformatics. 2020 Jun 22;21(1):257. doi: 10.1186/s12859-020-03585-4. PMID: 32571209; PMCID: PMC7310028.

LEMMI – Live Evaluation of Computational Methods for Metagenome Investigation

LEMMI

:: DESCRIPTION

LEMMI is the first-of-its-kind continuous benchmarking platform for metagenomics classifiers, featuring multi-objective ranking, and effective distribution of containerised software.

::DEVELOPER

Prof Zdobnov Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Seppey M, Manni M, Zdobnov EM.
LEMMI: a continuous benchmarking platform for metagenomics classifiers.
Genome Res. 2020 Aug;30(8):1208-1216. doi: 10.1101/gr.260398.119. Epub 2020 Jul 2. PMID: 32616517; PMCID: PMC7462069.

Admixem v1.0.2.2 – Quality Assessment Tool for Metagenome Assemblies

Admixem v1.0.2.2

:: DESCRIPTION

Admix’em (Admixture simulator) is a new forward-time simulator that allows for rapid and realistic simulations of admixed populations with selection.

::DEVELOPER

Ray Cui

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX
  • C++ COmpiler

:: DOWNLOAD

 Admixem

:: MORE INFORMATION

Citation

Admix’em: A flexible framework for forward-time simulations of hybrid populations with selection and mate choice.
Cui R, Schumer M, Rosenthal GG.
Bioinformatics. 2015 Nov 28. pii: btv700.

PyroTrimmer 1.1 – Preprocessor of Metagenome Sequences

PyroTrimmer 1.1

:: DESCRIPTION

PyroTrimmer is a program that trims barcodes, linkers, primers, and sequence region with low quality scores from 454 sequence reads.

::DEVELOPER

PyroTrimmer team

:: SCREENSHOTS

PyroTrimmer

:: REQUIREMENTS

  • Windows/Linux
  • Java

:: DOWNLOAD

 PyroTrimmer

:: MORE INFORMATION

Citation

J Microbiol. 2012 Oct;50(5):766-9. doi: 10.1007/s12275-012-2494-6.
PyroTrimmer: a software with GUI for pre-processing 454 amplicon sequences.
Oh J1, Kim BK, Cho WS, Hong SG, Kim KM.

DeepARG 1.0.2 – Deep Learning Approach for Predicting Antibiotic Resistance Genes in Metagenomes

DeepARG 1.0.2

:: DESCRIPTION

DeepARG is a machine learning solution that uses deep learning to characterize and annotate antibiotic resistance genes in metagenomes. It is composed of two models for two types of input: short sequence reads and gene-like sequences.

::DEVELOPER

Professor Zhang Liqing’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

DeepARG

:: MORE INFORMATION

Citation

Arango-Argoty G, Garner E, Pruden A, Heath LS, Vikesland P, Zhang L.
DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data.
Microbiome. 2018 Feb 1;6(1):23. doi: 10.1186/s40168-018-0401-z. PMID: 29391044; PMCID: PMC5796597.

Spherical – An iterative approach for Large Metagenome Assemblies

Spherical

:: DESCRIPTION

Spherical is an iterative approach to assembling metagenomic datasets. Spherical has been designed to produce a more complete assembly from deep sequenced metagenomic data.

::DEVELOPER

The Creevey Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

Spherical

:: MORE INFORMATION

Citation

Hitch, Thomas CA, and Christopher J. Creevey.
Spherical: an iterative workflow for assembling metagenomic datasets.
BMC bioinformatics 19.1 (2018): 20.”

crAss v2.2 – Cross-Assembly of Metagenomes

crAss v2.2

:: DESCRIPTION

crAss is a web tool for comparative metagenomics using cross-assembly.

::DEVELOPER

the Edwards Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac OsX / Linux /
  • Perl

:: DOWNLOAD

crAss

:: MORE INFORMATION

Citation:

Reference-independent comparative metagenomics using cross-assembly: crAss
Bas E. Dutilh, Robert Schmieder, Jim Nulton, Ben Felts, Peter Salamon, Robert A. Edwards and John L. Mokili
Bioinformatics 28: 3225-3231 (2012).

FOCUS 1.4 – A model to Identify Organisms present in Metagenomes

FOCUS 1.4

:: DESCRIPTION

FOCUS, an innovative and agile composition based using non-negative least squares to profile and report abundant organisms present in me-tagenomic samples and their relative abundance without sequence length dependencies.

::DEVELOPER

the Edwards Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac OsX / Linux
  • Python

:: DOWNLOAD

 FOCUS

:: MORE INFORMATION

Citation:

Silva, G. G. Z., D. A. Cuevas, B. E. Dutilh, and R. A. Edwards, 2014
FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares.
PeerJ, 2, e425, doi:10.7717/peerj.425.

MetaCompass v2.0-beta – Reference-guided Assembly of Metagenomes

MetaCompass v2.0-beta

:: DESCRIPTION

MetaCompass represents the first effective approach for reference-guided metagenomic assembly of low-abundance bacterial genomes that can complement and improve upon de novo metagenomic assembly methods.

::DEVELOPER

Treangen Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

MetaCompass

:: MORE INFORMATION