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

AutoSequin – automatically Annotate Sequences for Bulk Submission to GenBank

AutoSequin

:: DESCRIPTION

AutoSequin is designed to speed up the process of submitting HIV sequences to GenBank via NCBI’s Sequin program. It is ideal for the batch sequence submission. It makes a special formated table required for running NCBI’s tbl2asn program to generate .sqn file for submission to GenBank.

::DEVELOPER

Mullins Molecular Retrovirology Lab, University of Washington.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Perl

:: DOWNLOAD

 AutoSequin

:: MORE INFORMATION

MetaCSST – Metagemonic Complex Sequence Scanning Tool

MetaCSST

:: DESCRIPTION

MetaCSST is a tool to predict DGRs in sequenced genomes as well as metagenomic datasets. It is based on Generalized Hidden Markov Model (GHMM), using motif patterns to identify the elements in DGRs

::DEVELOPER

Dr. Chaochun Wei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

MetaCSST

:: MORE INFORMATION

Poretools 0.6.0 – A Toolkit for Analyzing Nanopore Sequence data

Poretools 0.6.0

:: DESCRIPTION

Poretools is a flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis.

::DEVELOPER

The Quinlan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Python

:: DOWNLOAD

 Poretools

:: MORE INFORMATION

Citation:

Poretools: a toolkit for analyzing nanopore sequence data.
Loman NJ, Quinlan AR.
Bioinformatics. 2014 Aug 20. pii: btu555.

Nexalign 1.35 – Aligns Sequences to Databases

Nexalign 1.35

:: DESCRIPTION

Nexalign is a program to align millions of short reads from next-generation sequencing data sets to reference genomes.

::DEVELOPER

FANTOM

:: SCREENSHOTS

N/A

: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Nexalign

:: MORE INFORMATION

SBT / SSBT 0.1 – (Split) Sequence Bloom Tree

SBT / SSBT 0.1

:: DESCRIPTION

The SBT (Sequence Bloom Tree) is a method that will allow you to index a set of
short-read sequencing experiments and then query them quickly for a given
sequence

SSBT is a method that will allow you to index a set of short-read sequencing experiments and then query them quickly for a given sequence.

::DEVELOPER

Kingsford Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOs
  • GCC
  • Jellyfish

:: DOWNLOAD

SBT / SSBT

:: MORE INFORMATION

Citation

Brad Solomon, Carl Kingsford (2016).
Fast search of thousands of short-read sequencing experiments.
Nature Biotechnology 34:300-302.

J Comput Biol. 2018 Jul;25(7):755-765. doi: 10.1089/cmb.2017.0265. Epub 2018 Mar 12.
Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence Bloom Trees.
Solomon B, Kingsford C

Seq-Gen 1.3.4 – Simulate the Evolution of Sequences along a Phylogeny

Seq-Gen 1.3.4

:: DESCRIPTION

Seq-Gen is a program that will simulate the evolution of nucleotide or amino acid sequences along a phylogeny, using common models of the substitution process. A range of models of molecular evolution are implemented including the general reversible model. State frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree. Thus large sets of replicate simulations can be easily created. It has been designed to be a general purpose simulator that incorporates most of the commonly used (and computationally tractable) models of molecular sequence evolution.

::DEVELOPER

Andrew Rambaut Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOS

:: DOWNLOAD

Seq-Gen

:: MORE INFORMATION

Citation

Comput Appl Biosci. 1997 Jun;13(3):235-8.
Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees.
Rambaut A1, Grassly NC.

SeCaPr v1.1.15 – SEquence CApture PRocessor

SeCaPr v1.1.15

:: DESCRIPTION

SeCaPr is a computational pipeline for processing Illumina sequence capture data

::DEVELOPER

Antonelli Lab

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux /  MacOsX
  • Python

:: DOWNLOAD

SeCaPr

:: MORE INFORMATION

Citation

PeerJ. 2018 Jul 13;6:e5175. doi: 10.7717/peerj.5175. eCollection 2018.
SECAPR-a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments.
Andermann T, Cano á, Zizka A, Bacon C, Antonelli A

EvolveAGene 4.02 – DNA Coding Sequence Evolution Simulation program

EvolveAGene 4.02

:: DESCRIPTION

EvolveAGene is a DNA coding sequence evolution simulation program.

::DEVELOPER

Barry G. Hall

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX

:: DOWNLOAD

  EvolveAGene

:: MORE INFORMATION

Citation

Mol Biol Evol. 2008 Apr;25(4):688-95. doi: 10.1093/molbev/msn008. Epub 2008 Jan 12.
Simulating DNA coding sequence evolution with EvolveAGene 3.
Hall BG.

Patser v3e – Find Locations of Patterns in Sequence

Patser v3e

:: DESCRIPTION

Patser scores the L-mers (subsequences of length L) of the indicated sequences against the indicated alignment or weight matrix.

::DEVELOPER

Stormo Lab in Department of Genetics, Washington University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • CCompiler

:: DOWNLOAD

 Patser

:: MORE INFORMATION