Tag: Exome

MendelScan 1.2.2 – Analyze Exome data for Mendelian Disorders

MendelScan 1.2.2

:: DESCRIPTION

MendelScan is a software package for analyzing targeted, whole-exome, or whole-genome sequencing data in family studies of inherited disease. Given the variant calls for a family (VCF file) and pedigree/phenotype information, MendelScan allows you to prioritize candidate variants based upon segregation, annotation, population frequency, and gene expression information. It also enables the mapping of disease genes using two novel algorithms: rare heterozygote rule out (RHRO) and shared identity-by-descent (SIBD).

::DEVELOPER

The Genome Institute at Washington University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Java

:: DOWNLOAD

 MendelScan

:: MORE INFORMATION

Citation:

Am J Hum Genet. 2014 Mar 6;94(3):373-84. doi: 10.1016/j.ajhg.2014.01.016. Epub 2014 Feb 20.
Exome-based mapping and variant prioritization for inherited Mendelian disorders.
Koboldt DC, Larson DE, Sullivan LS, Bowne SJ, Steinberg KM, Churchill JD, Buhr AC, Nutter N, Pierce EA, Blanton SH, Weinstock GM, Wilson RK, Daiger SP

RUbioSeq 3.8.1 – Parallelized pipelines to automate Exome Variation and Bisulfite-seq Analyses

RUbioSeq 3.8.1

:: DESCRIPTION

RUbioSeq has been developed to facilitate the primary and secondary analysis of resequencing projects by providing an integrated software suite of parallelized pipelines to detect exome variants (SNVs and CNVs) and to perform Bisulfite-seq analyses automatically.

::DEVELOPER

Miriam Rubio-Camarillo at Spanish National Cancer Research Centre (CNIO)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • Java
  • Samtools
  • Fastqc

:: DOWNLOAD

 RUbioSeq

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jul 1;29(13):1687-9. doi: 10.1093/bioinformatics/btt203. Epub 2013 Apr 28.
RUbioSeq: a suite of parallelized pipelines to automate exome variation and bisulfite-seq analyses.
Rubio-Camarillo M, Gómez-López G, Fernández JM, Valencia A, Pisano DG.

ADTEx 2.0 – Aberration Detection in Tumour Exome

ADTEx 2.0

:: DESCRIPTION

ADTEx is a freely available software package coded using R statistical language and Python to detect somatic copy number variations (CNVs) and genotypes in tumour whole exome samples. ADTEx is suitable for paired tumour/matched normal samples.

::DEVELOPER

Kaushalya Amarasinghe <kaushalya.amarasinghe@unimelb.edu.au>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R
  • Python
  • BedTOol

:: DOWNLOAD

 ADTEx

:: MORE INFORMATION

Citation:

BMC Genomics. 2014 Aug 28;15:732. doi: 10.1186/1471-2164-15-732.
Inferring copy number and genotype in tumour exome data.
Amarasinghe KC, Li J, Hunter SM, Ryland GL, Cowin PA, Campbell IG, Halgamuge SK

Jannovar 0.36 – A Java library for Exome Annotation

Jannovar 0.36

:: DESCRIPTION

Jannovar is a stand-alone Java application as well as a Java library designed to be used in larger software frameworks for exome analysis. Jannovar uses an interval tree to identify all transcripts affected by a given variant, and provides HGVS-compliant annotations for both for variants affecting coding sequences and splice junctions as well as UTR sequences and non-coding RNA transcripts. Jannovar can also perform family-based pedigree analysis with VCF files with data from members of a family segregating a Mendelian disorder. Using a desktop computer, Jannovar requires a few seconds to annotate a typical VCF file with exome data.

::DEVELOPER

The Computational Biology @ Charité Berlin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 Jannovar

:: MORE INFORMATION

Citation

Hum Mutat. 2014 May;35(5):548-55. doi: 10.1002/humu.22531. Epub 2014 Apr 9.
Jannovar: a java library for exome annotation.
Jäger M1, Wang K, Bauer S, Smedley D, Krawitz P, Robinson PN.

FSuite 1.0.4 – Exploiting Inbreeding in dense SNP chip and Exome data

FSuite 1.0.4

:: DESCRIPTION

FSuite is an integrative solution to exploit inbreeding in dense SNP chip and exome data. Its goals are for

  1. Population genetic studies:

    • estimating and detecting inbreeding on individuals without known genealogy,

    • estimating the individual probability to be into offspring of different mating types,

    • estimating the proportion of mating types in the population,

  2. Rare disease studies: performing homozygosity mapping with heterogeneity,

  3. Multifactorial disease studies: performing HBD-GWAS strategy.

::DEVELOPER

FSuite team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /MacOsX

:: DOWNLOAD

FSuite

:: MORE INFORMATION

Citation

Gazal S, Sahbatou M, Babron MC, Génin E, Leutenegger AL.
FSuite: exploiting inbreeding in dense SNP chip and exome data.
Bioinformatics. 2014 Jul 1;30(13):1940-1. doi: 10.1093/bioinformatics/btu149. Epub 2014 Mar 14. PMID: 24632498.

cnvOffSeq 0.1.2 – Detecting & Genotyping intergenic CNVs using off-target Exome data

cnvOffSeq 0.1.2

:: DESCRIPTION

cnvOffSeq is a set of Java-based command-line tools for detecting and genotyping intergenic copy number variation (CNV) using off-target data from whole-exome sequencing experiments.

::DEVELOPER

cnvOffSeq team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Mac OsX / Linux /Windows
  • Java

:: DOWNLOAD

 cnvOffSeq

:: MORE INFORMATION

Citation:

cnvOffSeq: detecting intergenic copy number variation using off-target exome sequencing data.
Bellos E, Coin LJ.
Bioinformatics. 2014 Sep 1;30(17):i639-i645.

ExomePeak 2.17.0 – Exome-based Analysis for RNA Epigenome Sequencing Data

ExomePeak 2.17.0

:: DESCRIPTION

ExomePeak is a software for affinity-based RNA epigenome sequencing data obtained from MeRIP-seq or m6A-seq

::DEVELOPER

ExomePeak team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/ Windows/MacOsX
  • R pacakge/MatLab
  • BioConductor

:: DOWNLOAD

 ExomePeak

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jun 15;29(12):1565-7. doi: 10.1093/bioinformatics/btt171. Epub 2013 Apr 14.
Exome-based analysis for RNA epigenome sequencing data.
Meng J1, Cui X, Rao MK, Chen Y, Huang Y.

XHMM 20140711 – eXome-Hidden Markov Model

XHMM 20140711

:: DESCRIPTION

The XHMM C++ software suite was written to call copy number variation (CNV) from next-generation sequencing projects, where exome capture was used (or targeted sequencing, more generally).

::DEVELOPER

Purcell Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 XHMM

:: MORE INFORMATION

Citation

Using XHMM Software to Detect Copy Number Variation in Whole-Exome Sequencing Data.
Fromer M, Purcell SM.
Curr Protoc Hum Genet. 2014 Apr 24;81:7.23.1-7.23.21. doi: 10.1002/0471142905.hg0723s81.

Mosdepth v0.2.6 – Fast BAM/CRAM Depth Calculation for WGS, Exome, or Targeted Sequencing

Mosdepth v0.2.6

:: DESCRIPTION

Mosdepth is a new command-line tool for rapidly calculating genome-wide sequencing coverage. It measures depth from BAM or CRAM files at either each nucleotide position in a genome or for sets of genomic regions.

::DEVELOPER

The Quinlan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

Mosdepth

:: MORE INFORMATION

Citation:

Bioinformatics. 2018 Mar 1;34(5):867-868. doi: 10.1093/bioinformatics/btx699.
Mosdepth: quick coverage calculation for genomes and exomes.
Pedersen BS, Quinlan AR.

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.