MCRL v1.01 – Metagenomic Clustering by Reference Library

MCRL v1.01

:: DESCRIPTION

MCLR is a data mining tool that can be used to probe a metagenome for homologs of a pre-defined reference library.

::DEVELOPER

MCRL team

:: SCREENSHOTS

N/A

::REQUIREMENTS

Linux
Matlab

:: DOWNLOAD

MCLR

:: MORE INFORMATION

Citation

Tadmor AD, Phillips R.
MCRL: using a reference library to compress a metagenome into a nonredundant list of sequences, considering viruses as a case study.
Bioinformatics. 2021 Oct 12:btab703. doi: 10.1093/bioinformatics/btab703. Epub ahead of print. PMID: 34636854.

metaSNV v2.0.1 – Metagenomic SNV Calling Pipeline

metaSNV v2.0.1

:: DESCRIPTION

MetaSNV is a pipeline for calling metagenomic single nucleotide variants (SNVs). It was designed to scale well with the exponentially increasing amount of available metagenomic datasets and is capable of handling large multi-species references.

::DEVELOPER

metaSNV team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX
Python

:: DOWNLOAD

metaSNV

:: MORE INFORMATION

Citation:

Van Rossum T, Costea PI, Paoli L, Alves R, Thielemann R, Sunagawa S, Bork P.
metaSNV v2: detection of SNVs and subspecies in prokaryotic metagenomes.
Bioinformatics. 2021 Nov 17:btab789. doi: 10.1093/bioinformatics/btab789. Epub ahead of print. PMID: 34791031.

MINTIA v1.0 – Metagenomic INsertT BIoinformatic Annotation

MINTIA v1.0

:: DESCRIPTION

MINTIA is a software package enabling biologists to easily generate and analyze large metagenomic sequence sets, retrieved after activity-based screening. It filters reads, performs assembly, removes cloning vector, annotates open reading frames and generates user friendly reports as well as files ready for submission to international sequence repositories.

::DEVELOPER

MINTIA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web server
Perl

:: DOWNLOAD

MINTIA

:: MORE INFORMATION

Citation

Bardou P, Laguerre S, Maman Haddad S, Legoueix Rodriguez S, Laville E, Dumon C, Potocki-Veronese G, Klopp C.
MINTIA: a metagenomic INserT integrated assembly and annotation tool.
PeerJ. 2021 Sep 27;9:e11885. doi: 10.7717/peerj.11885. PMID: 34692239; PMCID: PMC8483015.

WGSQuikr 1.0.0 – Whole-genome Shotgun Metagenomic Classification

WGSQuikr 1.0.0

:: DESCRIPTION

WGSQuikr is a very rapid, whole-genome shotgun metagenomic reconstruction.

::DEVELOPER

WGSQuikr team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsX /Windows
MatLab

:: DOWNLOAD

WGSQuikr

:: MORE INFORMATION

Citation

PLoS One. 2014 Mar 13;9(3):e91784. doi: 10.1371/journal.pone.0091784. eCollection 2014.
WGSQuikr: fast whole-genome shotgun metagenomic classification.
Koslicki D, Foucart S, Rosen G.

AmphoraVizu – Chart Visualization for Metagenomic and Genomic Analysis tools AMPHORA2 and AmphoraNet

AmphoraVizu

:: DESCRIPTION

AmphoraVizu can visualize outputs generated by the metagenomic and genomic analysis tool AMPHORA2 or its webserver implementation AmphoraNet.

::DEVELOPER

PIT Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/ Linux/ MacOsX
Perl

:: DOWNLOAD

AmphoraVizu

:: MORE INFORMATION

Citation

Microb Ecol. 2015 Apr;69(3):695-7. doi: 10.1007/s00248-014-0502-6. Epub 2014 Oct 10.
Visual Analysis of the Quantitative Composition of Metagenomic Communities: the AmphoraVizu Webserver.
Kerepesi C1, Szalkai B, Grolmusz V.

AmphoraNet – Metagenomic and Genomic Analysis tool (AMPHORA2)

AmphoraNet

:: DESCRIPTION

AmphoraNet webserver implementation of the AMPHORA2 workflow for phylogenetic analysis of metagenomic shotgun sequencing data and genomic data

::DEVELOPER

PIT Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

AmphoraNet: the webserver implementation of the AMPHORA2 metagenomic workflow suite.
Kerepesi C, Bánky D, Grolmusz V.
Gene. 2014 Jan 10;533(2):538-40. doi: 10.1016/j.gene.2013.10.015

TAMER 1.0 – Taxonomic Assignment of Metagenomic Sequencing Reads

TAMER 1.0

:: DESCRIPTION

TAMER is an R package for accurate taxonomic assignment of metagenomic sequencing reads.

::DEVELOPER

Lingling An , Hongmei Jiang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows
R

:: DOWNLOAD

TAMER

:: MORE INFORMATION

Citation

PLoS One. 2012;7(10):e46450. doi: 10.1371/journal.pone.0046450. Epub 2012 Oct 1.
A statistical framework for accurate taxonomic assignment of metagenomic sequencing reads.
Jiang H1, An L, Lin SM, Feng G, Qiu Y.

Tax4Fun 0.3.1 – Predicting Functional Profiles from Metagenomic 16S rRNA data

Tax4Fun 0.3.1

:: DESCRIPTION

Tax4Fun is a open-source R package that predicts the functional capabilities of microbial communities based on 16S datasets.

::DEVELOPER

Department of Bioinformatics , University of Göttingen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows
R

:: DOWNLOAD

Tax4Fun

:: MORE INFORMATION

Citation

Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data.
Aßhauer KP, Wemheuer B, Daniel R, Meinicke P.
Bioinformatics. 2015 May 7. pii: btv287.

Xander – Gene-targeted Metagenomic Assembler

Xander

:: DESCRIPTION

Xander is a gene-targeted assembler tool.

::DEVELOPER

Xander team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Java
Python

:: DOWNLOAD

Xander

:: MORE INFORMATION

Citation

Xander: employing a novel method for efficient gene-targeted metagenomic assembly.
Wang Q, Fish JA, Gilman M, Sun Y, Brown CT, Tiedje JM, Cole JR.
Microbiome. 2015 Aug 5;3:32. doi: 10.1186/s40168-015-0093-6.

MRC – Metagenomic and Metatranscriptomic data and analysis Management Workflow

MRC

:: DESCRIPTION

MRC is a metagenomic and metatranscriptomic data and analysis management workflow. In brief, it interfaces with a database of protein families and classifies translated metagenomic/metatrnascriptomic sequence reads into families.

::DEVELOPER

Pollard Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
Perl
R

:: DOWNLOAD

MRC

:: MORE INFORMATION