OTUbase 1.42.0 – Operational Taxonomic Unit based analysis within R

OTUbase 1.42.0

:: DESCRIPTION

OTUbase is an R package designed to facilitate the analysis of operational taxonomic unit (OTU) data and sequence classification (taxonomic) data.

::DEVELOPER

Daniel Beck <danlbek at gmail.com>, Matt Settles

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows/ MacOsX
  • R

:: DOWNLOAD

  OTUbase

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jun 15;27(12):1700-1. doi: 10.1093/bioinformatics/btr196. Epub 2011 Apr 15.
OTUbase: an R infrastructure package for operational taxonomic unit data.
Beck D1, Settles M, Foster JA.

CROP 1.33 – Clustering 16S rRNA For OTU Prediction

CROP 1.33

:: DESCRIPTION

CROP is a clustering tool designed mainly for Metagenomics studies, which clusters 16S rRNA sequences into Operational Taxonomic Units (OTU).

::DEVELOPER

Ting Chen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GSL
  • C++ Compiler

:: DOWNLOAD

 CROP

:: MORE INFORMATION

Citation:

Xiaolin Hao; Rui Jiang; Ting Chen
Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering
Bioinformatics 2011; doi: 10.1093/bioinformatics/btq725

mOTUs 2.5.1 – Tool for Marker Gene-based OTU (mOTU) Profiling

mOTUs 2.5.1

:: DESCRIPTION

The mOTUs profiler is a computational tool that estimates relative abundance of known and currently unknown microbial community members using metagenomic shotgun sequencing data.

::DEVELOPER

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

mOTUs

:: MORE INFORMATION

Citation

Microbial abundance, activity and population genomic profiling with mOTUs2
Alessio Milanese, et al.
Nature Communications 10, Article number: 1014 (2019): https://doi.org/10.1038/s41467-019-08844-4

M-pick – Modularity-based Clustering method for OTU picking

M-pick

:: DESCRIPTION

M-pick is a modularity-based clustering method for OTU picking

::DEVELOPER

Xiaoyu Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 M-pick

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Feb 7;14:43. doi: 10.1186/1471-2105-14-43.
M-pick, a modularity-based method for OTU picking of 16S rRNA sequences.
Wang X1, Yao J, Sun Y, Mai V.

Otupipe 1.1.9 – OTU Clustering pipeline for Next-gen reads

Otupipe 1.1.9

:: DESCRIPTION

The otupipe script creates OTUs from next-generation sequence reads for single-region experiments such as 16S and ITS. Otupipe performs error-correction, amplicon and abundance estimation, chimera detection (using UCHIME) and OTU clustering.

::DEVELOPER

Robert Edgar

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 otupipe

:: MORE INFORMATION

SLP – Single-Linkage Preclustering for improved OTU clustering

SLP

:: DESCRIPTION

 SLP is a software for single-linkage preclustering for improved OTU clustering . It was based on pairwise distances this is used as a preliminary step before average linkage clustering of short (<250nt) sequences.

::DEVELOPER

The VAMPS project 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SLP

:: MORE INFORMATION

Citation:

Huse, SM, Mark Welch, D, Morrison, HG, and Sogin, ML (2010)
Ironing out the wrinkles in the rare biosphere through improved OTU clustering.
Environmental Microbiology (2010) 12(7), 1889-1898.