FILTUS 1.0.5 – Analysis of Exome Sequencing data

FILTUS 1.0.5

:: DESCRIPTION

FILTUS is a stand-alone tool for downstream analysis in high-throughput sequencing projects. It is especially well suited for identification of variants causing Mendelian disease.

::DEVELOPER

Magnus Dehli Vigeland, PhD

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX/ Windows
Python

:: DOWNLOAD

FILTUS

:: MORE INFORMATION

Citation

FILTUS: a desktop GUI for fast and efficient detection of disease-causing variants, including a novel autozygosity detector.
Vigeland MD, Gjøtterud KS, Selmer KK.
Bioinformatics. 2016 Jan 27. pii: btw046.

GIPS 1.7 – Gene Identification via Phenotype Sequencing

GIPS 1.7

:: DESCRIPTION

GIPS software considers a range of experimental and analysis choices in sequencing-based forward genetics studies within an integrated probabilistic framework, which enables direct gene cloning from the sequencing of several unrelated mutants of the same phenotype without the need to create segregation populations.

::DEVELOPER

GIPS team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / WIndows/ MacOsX
Java

:: DOWNLOAD

GIPS

:: MORE INFORMATION

Citation

GIPS: A Software Guide to Sequencing-based Direct Gene Cloning in Forward Genetics Studies.
Hu H, Wang W, Zhu Z, Zhu J, Tan D, Zhou Z, Mao C, Chen X.
Plant Physiol. 2016 Feb 3. pii: pp.01327.2015.

Resilience – Scan Sequencing or Genotyping Data for Potential unexpected Heroes

Resilience

:: DESCRIPTION

The Resilience Project aims at finding individuals with rare genetic mutations that the medical text books would indicate should have caused catastrophic illness but somehow these individuals are “resilient” – they have been protected via yet to be discovered genetic or environmental factors.

::DEVELOPER

Rong Chen Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows
JAVE

:: DOWNLOAD

Resilience

:: MORE INFORMATION

HPG pore – Framework for Nanopore Sequencing data

HPG pore

:: DESCRIPTION

HPG Pore is a toolkit to explore and analyze nanopore sequencing data that can run both on a single computer and on the Hadoop distributed computing framework.

::DEVELOPER

HPG pore team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

HPG pore

:: MORE INFORMATION

Citation:

HPG pore: an efficient and scalable framework for nanopore sequencing data.
Tarraga J, Gallego A, Arnau V, Medina I, Dopazo J.
BMC Bioinformatics. 2016 Feb 27;17(1):107. doi: 10.1186/s12859-016-0966-0.

Chimira 1.5 – Analysis of small RNA Sequencing data and microRNA modifications

Chimira 1.5

:: DESCRIPTION

Chimira is an online tool for analysing large amounts of small RNA-Seq data and acquiring their modifications profile.

::DEVELOPER

Chimira team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

Chimira: Analysis of small RNA Sequencing data and microRNA modifications.
Vitsios DM, Enright AJ.
Bioinformatics. 2015 Jun 20. pii: btv380.

miFRame – Analysis and Visualization of miRNA sequencing data in Neurological Disorders

miFRame

:: DESCRIPTION

miFRame which supports the analysis of human small RNA NGS data is a web server for analysis and visualization of miRNA sequencing data in neurological disorders.

::DEVELOPER

Chair for clinical bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

:: MORE INFORMATION

Citation:

J Transl Med. 2015 Jul 14;13:224. doi: 10.1186/s12967-015-0594-x.
miFRame: analysis and visualization of miRNA sequencing data in neurological disorders.
Backes C, Haas J, Leidinger P, Frese K, Großmann T, Ruprecht K, Meder B, Meese E, Keller A

CLOSE 20150928 – A Toolkit for CNA/LOH Analysis with Sequencing data

CLOSE 20150928

:: DESCRIPTION

CLOSE is a toolkit for CNA and LOH analysis (as well as CLOnality analysis) with SEquencing data.

::DEVELOPER

CLOSE team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOSX / Windows
R

:: DOWNLOAD

:: MORE INFORMATION

Citation

Global copy number profiling of cancer genomes.
Wang X, Chen M, Yu X, Pornputtapong N, Chen H, Zhang N, Powers RS, Krauthammer M.
Bioinformatics. 2015 Nov 16. pii: btv676.

deFUME 1.0 – Dynamic Exploration of Functional Metagenomics Sequencing Data

deFUME 1.0

:: DESCRIPTION

deFUME is an easy-to-use web-server for trimming, assembly and functional annotation of Sanger sequencing data derived from functional selection experiments.

::DEVELOPER

deFUME team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

deFUME

:: MORE INFORMATION

Citation

deFUME: Dynamic exploration of functional metagenomic sequencing data.
van der Helm E, Geertz-Hansen HM, Genee HJ, Malla S, Sommer MO.
BMC Res Notes. 2015 Jul 31;8:328. doi: 10.1186/s13104-015-1281-y.

GIGI-Pick 1.06 – Subject Selection for Sequencing in Pedigrees

GIGI-Pick 1.06

:: DESCRIPTION

GIGI-Pick is a computer program that facilitates the evaluation and comparison of subject selection choices in sequencing studies in pedigrees.

::DEVELOPER

Ellen M. Wijsman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++ Compiler

:: DOWNLOAD

GIGI-Pick

:: MORE INFORMATION

Citation:

Cheung CYK, Blue EM, Wijsman EM (2014)
A statistical framework to guide sequencing choices in pedigrees.
American Journal of Human Genetics 94:257-267.

SeqBuster 3.5 – small RNA analysis of deep Sequencing data

SeqBuster 3.5

:: DESCRIPTION

SeqBuster is a highly versatile and reliable web-based toolkit to process and analyze large-scale small RNA datasets.

::DEVELOPER

Estivill’s lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ MacOsX/ Windows
Java
mysql
R package

:: DOWNLOAD

SeqBuster

:: MORE INFORMATION

Citation

Specific Small-RNA Signatures in the Amygdala at Premotor and Motor Stages of Parkinson’s Disease Revealed by Deep Sequencing Analysis.
Pantano L, Friedländer MR, Escaramís G, Lizano E, Pallarès-Albanell J, Ferrer I, Estivill X, Martí E.
Bioinformatics. 2015 Nov 2. pii: btv632.

SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells.
Pantano L, Estivill X, Martí E.
Nucleic Acids Res. 2010 Mar;38(5):e34. doi: 10.1093/nar/gkp1127.