CLUSTOM-CLOUD 1.0.0 – CLUSTering 16S NGS Sequences by Overlap Minimization

CLUSTOM-CLOUD 1.0.0

:: DESCRIPTION

CLUSTOM-CLOUD that is categorized into hierarchical clustering approach is a program for clustering high-throughput 16S sequences with user-defined thresholds.

::DEVELOPER

CLUSTOM team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CLUSTOM

:: MORE INFORMATION

Citation

Oh J, Choi CH, Park MK, Kim BK, Hwang K, Lee SH, Hong SG, Nasir A, Cho WS, Kim KM.
CLUSTOM-CLOUD: In-Memory Data Grid-Based Software for Clustering 16S rRNA Sequence Data in the Cloud Environment.
PLoS One. 2016 Mar 8;11(3):e0151064. doi: 10.1371/journal.pone.0151064. PMID: 26954507; PMCID: PMC4783016.

CLUSTOM: a novel method for clustering 16S rRNA next generation sequences by overlap minimization.
Hwang K, Oh J, Kim TK, Kim BK, Yu DS, Hou BK, Caetano-Anollés G, Hong SG, Kim KM.
PLoS One. 2013 May 1;8(5):e62623. doi: 10.1371/journal.pone.0062623

Megraft 1.0.2 – Graft Ribosomal Small Subunit (16S/18S) Fragments onto full-length SSU Sequences

Megraft 1.0.2

:: DESCRIPTION

Megraft is a software package that grafts SSU (small subunit) fragments onto full-length SSU sequences, accounting for observed and unobserved variability, for accurate assessment of species richness and sequencing depth in metagenomics endeavors.

::DEVELOPER

The Bengtsson-Palme Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 Megraft

:: MORE INFORMATION

Citation:

Res Microbiol. 2012 Jul;163(6-7):407-12. doi: 10.1016/j.resmic.2012.07.001. Epub 2012 Jul 21.
Megraft: a software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes and similar environmental datasets.
Bengtsson J, Hartmann M, Unterseher M, Vaishampayan P, Abarenkov K, Durso L, Bik EM, Garey JR, Eriksson KM, Nilsson R

Vikodak – A Modular Framework for Inferring Functional Potential of Microbial Communities from 16S Metagenomic Datasets

Vikodak

:: DESCRIPTION

Vikodak (a word derived from Sanskrit language, which refers to ‘Decoder’) is a multi-modular package expected to bring significant value addition to currently available tools for 16S based functional inference.

::DEVELOPER

Vikodak team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Vikodak – A Modular Framework for Inferring Functional Potential of Microbial Communities from 16S Metagenomic Datasets.
Nagpal S, Haque MM, Mande SS.
PLoS One. 2016 Feb 5;11(2):e0148347. doi: 10.1371/journal.pone.0148347.

REAGO 1.1 – REconstruct 16S ribosomal RNA Genes from MetagenOmic data

REAGO 1.1

:: DESCRIPTION

REAGO is an assembly tool for 16S ribosomal RNA recovery from metagenomic data

::DEVELOPER

Cheng Yuan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 REAGO

:: MORE INFORMATION

Citation

Reconstructing 16S rRNA genes in metagenomic data.
Yuan C, Lei J, Cole J, Sun Y.
Bioinformatics. 2015 Jun 15;31(12):i35-i43. doi: 10.1093/bioinformatics/btv231.