Seal – SEquence ALignment Evaluation Suite

 Alignment / BLAST 0 views Comments Off on Seal – SEquence ALignment Evaluation Suite
Jul 012016
 

Seal 2.1

:: DESCRIPTION

Seal is a comprehensive sequencing simulation and alignment tool evaluation suite.

::DEVELOPER

Matt Ruffalo

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 Seal

:: MORE INFORMATION

Citation

Comparative analysis of algorithms for next-generation sequencing read alignment.
Ruffalo M, LaFramboise T, Koyutürk M.
Bioinformatics. 2011 Oct 15;27(20):2790-6. doi: 10.1093/bioinformatics/btr477

 Posted by at 5:56 pm

LoQuM 0.2 – LOgistic Regression tool for Calibrating the QUality of Short Read Mappings

 DNA / Genome Analysis 0 views Comments Off on LoQuM 0.2 – LOgistic Regression tool for Calibrating the QUality of Short Read Mappings
Jul 012016
 
LoQuM 0.2 - LOgistic Regression tool for Calibrating the QUality of Short Read Mappings

LoQuM 0.2 :: DESCRIPTION LoQuM assigns reliable mapping quality scores to mappings of Illumina reads returned by an alignment tool. ::DEVELOPER LoQuM team :: SCREENSHOTS N/A :: REQUIREMENTS Windows/Linux/MacOsX Python R :: DOWNLOAD  LoQuM :: MORE INFORMATION Citation Accurate estimation of short read mapping quality for next-generation genome sequencing. Ruffalo M, Koyutürk M, Ray S, […]

Pluribus / PluribusFast – Exploring the Limits of Error Correction Using a Suffix Tree

 DNA / Genome Analysis 0 views Comments Off on Pluribus / PluribusFast – Exploring the Limits of Error Correction Using a Suffix Tree
Jul 012016
 
Pluribus / PluribusFast - Exploring the Limits of Error Correction Using a Suffix Tree

Pluribus / PluribusFast :: DESCRIPTION Pluribus utilizes a suffix tree to identify and correct sequencing errors in next generation sequencing data. PluribusFast is a more efficient implementation of the Pluribus algorithm. ::DEVELOPER Pluribus team :: SCREENSHOTS N/A :: REQUIREMENTS Windows/Linux/MacOsX JRE :: DOWNLOAD  Pluribus / PluribusFast :: MORE INFORMATION Citation Pluribus – Exploring the Limits of Error […]

Ancestor v1.1 – Computational Inference of Ancestral Genomes

 DNA / Genome Analysis 5 views Comments Off on Ancestor v1.1 – Computational Inference of Ancestral Genomes
Jul 012016
 
Ancestor v1.1 - Computational Inference of Ancestral Genomes

Ancestor v1.1 :: DESCRIPTION Ancestors is a web server allowing one to easily and quickly perform the last three steps of the ancestral genome reconstruction procedure. ::DEVELOPER Abdoulaye Banire Diallo :: SCREENSHOTS N/A :: REQUIREMENTS Web Browser :: DOWNLOAD  NO :: MORE INFORMATION Citation Bioinformatics. 2010 Jan 1;26(1):130-1. doi: 10.1093/bioinformatics/btp600. Epub 2009 Oct 22. Ancestors […]

Jul 012016
 
BIGSdb 1.14.2 - Bacterial Isolate Genome Sequence Database

BIGSdb 1.14.2 :: DESCRIPTION BIGSdb is software designed to store and analyse sequence data for bacterial isolates. Any number of sequences can be linked to isolate records – these can be small contigs assembled from dideoxy sequencing through to whole genomes (complete or multiple contigs generated from parallel sequencing technologies such as 454 or Illumina Solexa). […]

LedPred 1.4.0 – Learning from DNA to Predict enhancers

 DNA / Genome Analysis 15 views Comments Off on LedPred 1.4.0 – Learning from DNA to Predict enhancers
Jul 012016
 
LedPred 1.4.0 - Learning from DNA to Predict enhancers

LedPred 1.4.0 :: DESCRIPTION LedPred aims at creating a predictive model of regulatory sequences used to score unknown sequences based on the content of DNA motifs, next-generation sequencing (NGS) peaks and signals and other numerical scores of the sequences using supervised classification. ::DEVELOPER Elodie Darbo, Denis Seyres, Aitor Gonzalez<aitor.gonzalez at univ-amu.fr> :: SCREENSHOTS N/A :: REQUIREMENTS […]

MiXCR 1.8.1 – Analysis of T- and B- cell Receptor Repertoire Sequencing data

 DNA / Genome Analysis 44 views Comments Off on MiXCR 1.8.1 – Analysis of T- and B- cell Receptor Repertoire Sequencing data
Jul 012016
 
MiXCR 1.8.1 - Analysis of T- and B- cell Receptor Repertoire Sequencing data

MiXCR 1.8.1 :: DESCRIPTION MiXCR is an universal software for fast and accurate analysis of T- and B- cell receptor repertoire sequencing data ::DEVELOPER MiLaboratory :: SCREENSHOTS N/A :: REQUIREMENTS Windows/ Linux / MacOsX JRE :: DOWNLOAD  MiXCR :: MORE INFORMATION Citation: Nat Methods. 2015 May;12(5):380-1. doi: 10.1038/nmeth.3364. MiXCR: software for comprehensive adaptive immunity profiling. Bolotin […]

VDJtools 1.0.9 – Post-analysis of Immune Repertoire Sequencing data

 DNA / Genome Analysis 34 views Comments Off on VDJtools 1.0.9 – Post-analysis of Immune Repertoire Sequencing data
Jul 012016
 
VDJtools 1.0.9 - Post-analysis of Immune Repertoire Sequencing data

VDJtools 1.0.9 :: DESCRIPTION VDJtools is a comprehensive framework for post-analysis of immune repertoire sequencing data. ::DEVELOPER Mikhail Shugay :: SCREENSHOTS N/A :: REQUIREMENTS Windows/ Linux JRE :: DOWNLOAD  VDJtools :: MORE INFORMATION Citation: VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires. Shugay M, Bagaev DV, Turchaninova MA, Bolotin DA, Britanova OV, Putintseva EV, Pogorelyy MV, […]

PALEOMIX 1.2.5 – Characterization of Ancient and Modern Genomes by SNP Detection and Phylogenomic and Metagenomic analysis

 DNA / Genome Analysis 49 views Comments Off on PALEOMIX 1.2.5 – Characterization of Ancient and Modern Genomes by SNP Detection and Phylogenomic and Metagenomic analysis
Jul 012016
 
PALEOMIX 1.2.5 - Characterization of Ancient and Modern Genomes by SNP Detection and Phylogenomic and Metagenomic analysis

PALEOMIX 1.2.5 :: DESCRIPTION The PALEOMIX pipeline is a user-friendly package designed for Unix-like systems and largely automates the analyses related to whole genome re-sequencing. It is compatible with a full range of sequence data and performs a series of user-defined analyses, including read trimming, collapsing of overlapping mate-pairs, read mapping, PCR duplicate removal, SNP […]

Jul 012016
 
nucleR 2.4.0 - Non-parametric Nucleosome Positioning

nucleR 2.4.0 :: DESCRIPTION nucleR is an R/Bioconductor package for a flexible and fast recognition of nucleosome positioning from next generation sequencing and tiling arrays experiments. ::DEVELOPER Molecular Modeling and Bioinformatics Unit , IRB Barcelona :: SCREENSHOTS N/A :: REQUIREMENTS Linux / MacOsX / Windows R BioConductor :: DOWNLOAD  nucleR :: MORE INFORMATION Citation Oscar […]