PhyloAssigner 6.166 – Phylogenetic Classification of Amplicon Pyrosequences

PhyloAssigner 6.166

:: DESCRIPTION

PhyloAssigner is a Perl pipeline for phylogenetic classification of amplicon pyrosequences.

::DEVELOPER

Bioinformatics at AWI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

PhyloAssigner

:: MORE INFORMATION

Citation

ISME J. 2013 Jul;7(7):1322-32. doi: 10.1038/ismej.2013.32.
High-resolution SAR11 ecotype dynamics at the Bermuda Atlantic Time-series Study site by phylogenetic placement of pyrosequences.
Vergin KL1, Beszteri B, Monier A, Thrash JC, Temperton B, Treusch AH, Kilpert F, Worden AZ, Giovannoni SJ.

SESAME 1.0 – Analyze Amplicon Sequences obtained through NGS Technologies

SESAME 1.0

:: DESCRIPTION

SESAME (SEquence Seeker and AMplicon Explorer)is a user friendly web application package for analyzing amplicon sequences obtained through NGS technologies. It was tested extensively with Mozilla Firefox 3.5 and Chrome web browsers. It is designed to provide individual amplicon alignments so the user(s) can easily validate alleles and distinguish them from sequencing errors and artifacts. It includes automatic sequence assignation to multiple loci and samples via oligonucleotides tags. An assistant guides the user for input data upload and through the automatic sequence analysis steps. It provides an intuitive point-and-click interface to validate sequences as alleles from amplicon sequences alignments. All data are stored in a relational database, that user can query or filter through an intuitive interface. The results are exported as genotypes or sequences of genetic variants.

::DEVELOPER

 the Next Generation Sequencing @ CBGP.

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 SESAME

:: MORE INFORMATION

Citation

Meglécz E., Piry S., Desmarais E., Galan M., Gilles A., Guivier E., Pech N. and Martin J.-F. (2010).
SESAME (SEquence Seeker & AMplicon Explorer): Genotyping based on high-throughput multiplex amplicon sequencing.
Bioinformatics. 2011 Jan 15;27(2):277-8

VARIFI – Variant Identification, Filtering and Annotation of Amplicon Sequencing Data

VARIFI

:: DESCRIPTION

VARIFI is a pipeline for finding reliable genetic variants (single nucleotide polymorphisms (SNPs) and insertions and deletions (indels)).

::DEVELOPER

the Center of Integrative Bioinformatics Vienna (CIBIV)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

VARIFI-Web-Based Automatic Variant Identification, Filtering and Annotation of Amplicon Sequencing Data.
Krunic M, Venhuizen P, Müllauer L, Kaserer B, von Haeseler A.
J Pers Med. 2019 Feb 1;9(1). pii: E10. doi: 10.3390/jpm9010010.

dbcAmplicons 0.6.7 – Analysis of Double Barcoded Illumina Amplicon Data

dbcAmplicons 0.6.7

:: DESCRIPTION

dbcAmplicons is a python application for processing massively multiplexed Illumina amplicon runs.

::DEVELOPER

Matt Settles

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows/ MacOsX
  • Python

:: DOWNLOAD

 dbcAmplicons

:: MORE INFORMATION

PCR Analyzer v 1.02 – Estimate for Initial Amount of Amplicon Present in a PCR

PCR Analyzer v 1.02

:: DESCRIPTION

PCR Analyzer is a software to estimate the initial amount of amplicon using a simplified mechanistic model based on chemical reactions in the annealing step of the PCR.

::DEVELOPER

National Institute of Environmental Health Sciences , National Institute of Health

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

PCR Analyzer

:: MORE INFORMATION

Citation

Marjo V Smith , Chris R Miller, Michael Kohn, Nigel J Walker and Chris J Portier
Absolute estimation of initial concentrations of amplicon in a real-time RT-PCR process
BMC Bioinformatics 2007, 8:409doi:10.1186/1471-2105-8-409

PANGEA 1.0.2 – Pipeline Analysis for Next GEneration Amplicons

PANGEA 1.0.2

:: DESCRIPTION

PANGEA is a code useful for the analysis of 16S rRNA nucleotide sequences

::DEVELOPER

University of Florida Genetics Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Perl

:: DOWNLOAD

 PANGEA

:: MORE INFORMATION

Citation

ISME J. 2010 Jul;4(7):852-61. doi: 10.1038/ismej.2010.16. Epub 2010 Feb 25.
PANGEA: pipeline for analysis of next generation amplicons.
Giongo A1, Crabb DB, Davis-Richardson AG, Chauliac D, Mobberley JM, Gano KA, Mukherjee N, Casella G, Roesch LF, Walts B, Riva A, King G, Triplett EW.

MetAmp – Meta-amplicon Analysis

MetAmp

:: DESCRIPTION

MetAmp tool is developed for analysis of amplicon data by combining several marker regions from 16S rRNA genes. Such marker regions serve as unique identificators for species.

::DEVELOPER

Ilya Zhbannikov

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 MetAmp

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Jan 27. pii: btv049.
MetAmp: combining amplicon data from multiple markers for OTU analysis.
Zhbannikov IY, Foster JA

DAFGA 1.0 – Diversity Analysis of Functional Gene Amplicons

DAFGA 1.0

:: DESCRIPTION

DAFGA estimates the evolutionary rate of a particular functional gene in a standardized manner by relating its sequence divergence to that of the 16S rRNA gene.

::DEVELOPER

Yongkyu Kim (yongkyu.kim@mpi-marburg.mpg.de.)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • FastTree
  • emboss
  • Muscle
  • BLAST+

:: DOWNLOAD

 DAFGA

:: MORE INFORMATION

Citation

DAFGA: Diversity Analysis of Functional Gene Amplicons.
Kim Y, Liesack W.
Bioinformatics. 2014 Jun 17. pii: btu394.

Amplicon b09 – Software for Designing PCR Primers on Aligned DNA Sequences

Amplicon b09

:: DESCRIPTION

 Amplicon is a tool for designing PCR primers where groups of related DNA sequences can be assessed in aligned form. This is especially useful for designing ‘group-specific’ PCR primer sets that produce amplicons from a targer group of species, but not from other groups of species. Amplicon assists in group-specific PCR primer desing primarily by being a visualisation tool for alignments from which the user can select regions that may be group-specific primer binding sites. Other useful features that are not common in other PCR primer design software are handling of gapped sequences and degenerate sites in aligned DNA. Group-specific PCR primer sets are useful in a wide variety of situation where environmental DNA is being examined and the diversity or identity of some of the DNA sequences within a sample need to be determined.

::DEVELOPER

Dr Simon Jarman

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

  Amplicon 

:: MORE INFORMATION

Citation

Jarman SN (2004)
Amplicon: software for designing PCR primers on aligned DNA sequences.
Bioinformatics 20: 1644-1645.