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.

CLAMMS 1.1 – A CNV-calling algorithm for Exome Sequencing data

CLAMMS 1.1

:: DESCRIPTION

CLAMMS (Copy number estimation using Lattice-Aligned Mixture Models) is an algorithm for calling copy number variants (CNVs) from exome sequencing read depths.

::DEVELOPER

Regeneron Genetics Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

CLAMMS

:: MORE INFORMATION

Citation:

CLAMMS: a scalable algorithm for calling common and rare copy number variants from exome sequencing data.
Packer JS, Maxwell EK, O’Dushlaine C, Lopez AE, Dewey FE, Chernomorsky R, Baras A, Overton JD, Habegger L, Reid JG.
Bioinformatics. 2015 Sep 17. pii: btv547.

Cpipe 2.5.1 – Exome Sequencing Pipeline

Cpipe 2.5.1

:: DESCRIPTION

Cpipe is a variant detection pipeline designed to process high throughput sequencing data (sometimes called “next generation sequencing” data), with the purpose of identifying potentially pathogenic mutations.

::DEVELOPER

the Melbourne Genomics Health Alliance

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Java

:: DOWNLOAD

 Cpipe

:: MORE INFORMATION

Citation:

Cpipe: a shared variant detection pipeline designed for diagnostic settings.
Sadedin SP, Dashnow H, James PA, Bahlo M, Bauer DC, Lonie A, Lunke S, Macciocca I, Ross JP, Siemering KR, Stark Z, White SM; Melbourne Genomics Health Alliance, Taylor G, Gaff C, Oshlack A, Thorne NP.
Genome Med. 2015 Jul 10;7(1):68. doi: 10.1186/s13073-015-0191-x.

Jannovar 0.15 – A Java library for Exome Annotation

Jannovar 0.15

:: 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 at the Institute for Medical Genetics and Human Genetics at Charité-Universitätsmedizin 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.

XomAnnotate – a Meta-analysis and Functional-analysis software for Exome

XomAnnotate

:: DESCRIPTION

XomAnnotate is a meta-analysis and functional-analysis pipeline for heterogeneous and complex exome. It combines GATK UnifiedGenotyper, Freebayes, Delly, and Lumpy algorithms that were designed for whole-genome and combines their strengths for exome data through meta-analysis to identify comprehensive mutation profile (SNPs, short inserts/deletes, and structural variations) of patients.

::DEVELOPER

XomAnnotate team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 XomAnnotate

:: MORE INFORMATION

Citation:

XomAnnotate: Analysis of Heterogeneous and Complex Exome- A Step towards Translational Medicine.
Talukder AK, Ravishankar S, Sasmal K, Gandham S, Prabhukumar J, Achutharao PH, Barh D, Blasi F.
PLoS One. 2015 Apr 23;10(4):e0123569. doi: 10.1371/journal.pone.0123569.