Tag: Exome Sequencing

SIMPLEX 2.0 – Cloud-enabled pipeline for the comprehensive analysis of Exome Sequencing data

SIMPLEX 2.0

:: DESCRIPTION

SIMPLEX is a cloud-enabled autonomous analysis pipeline, which comprises the complete exome analysis workflow. The pipeline combines several in-house developed and published applications to perform the following steps: (a) initial quality control, (b) intelligent data filtering and pre-processing, (c) sequence alignment to a reference genome, (d) SNP and DIP detection, (e) functional annotation of variants using different approaches, and (f) detailed report generation during various stages of the workflow.

::DEVELOPER

the Division of Bioinformatics, Innsbruck Medical University

:: SCREENSHOTS

 N/A

:: REQUIREMENTS

:: DOWNLOAD

 SIMPLEX

 :: MORE INFORMATION

Citation

SIMPLEX: cloud-enabled pipeline for the comprehensive analysis of exome sequencing data.
Fischer M, Snajder R, Pabinger S, Dander A, Schossig A, Zschocke J, Trajanoski Z, Stocker G.
PLoS One. 2012;7(8):e41948. doi: 10.1371/journal.pone.0041948.

SeqBench 1.0 – Integrated Solution for the Management and Analysis of Exome Sequencing data

SeqBench 1.0

:: DESCRIPTION

SeqBench, a web-based application, combines management and analysis of exome sequencing data into one solution. It provides a user friendly data acquisition module to facilitate comprehensive and intuitive data handling.

::DEVELOPER

the Division of Bioinformatics, Innsbruck Medical University

:: SCREENSHOTS

 N/A

:: REQUIREMENTS

:: DOWNLOAD

 SeqBench,

 :: MORE INFORMATION

Citation

BMC Res Notes. 2014 Jan 20;7:43. doi: 10.1186/1756-0500-7-43.
SeqBench: integrated solution for the management and analysis of exome sequencing data.
Dander A1, Pabinger S, Sperk M, Fischer M, Stocker G, Trajanoski Z.

MitoSeek 1.3 – Extract Mitochondrial Genome information from Exome Sequencing data

MitoSeek 1.3

:: DESCRIPTION

MitoSeek is an open-source software tool to reliably and easily extract mitochondrial genome information from exome sequencing data. MitoSeek evaluates mitochondrial genome alignment quality, estimates relative mitochondrial copy numbers, and detects heteroplasmy, somatic mutation, and structural variance of the mitochondrial genome.

::DEVELOPER

Jiang (River) Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 MitoSeek

:: MORE INFORMATION

Citation

Yan Guo, Jiang Li, Yu Shyr, David C. Samuels.
MitoSeek: Extracting Mitochondria Information and Performing High Throughput Mitochondria Sequencing Analysis.
Bioinformatics (2013) 29 (9): 1210-1211

CANOES 0.1 – Detecting CNVs from Exome Sequencing data

CANOES 0.1

:: DESCRIPTION

CANOES is a new method to call CNVs from exome sequencing data with arbitrary number of reference samples.

::DEVELOPER

Shen Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • R

:: DOWNLOAD

  CANOES

:: MORE INFORMATION

Citation

Backenroth D, Homsy J, Murillo LR, Glessner J, Lin E, Brueckner M, Lifton R, Goldmuntz E, Chung WK, Shen Y.
CANOES: detecting rare copy number variants from whole exome sequencing data.
Nucleic Acids Res. 2014 Jul;42(12):e97. doi: 10.1093/nar/gku345. Epub 2014 Apr 25. PMID: 24771342; PMCID: PMC4081054.

FishingCNV 2.1 – Detecting rare Copy Number Variations in Exome-sequencing data

FishingCNV 2.1

:: DESCRIPTION

FishingCNV is a tool for comprehensive analysis of rare copy number variations in high-throughput exome sequencing data. The inputs are standard coverage files produced by Genome Analysis ToolKit (GATK), and the output is a file containing putative CNVs.

::DEVELOPER

Yuhao Shi (yuhao.shi@mail.mcgill.ca)

:: SCREENSHOTS

FishingCNV

:: REQUIREMENTS

  • Linux /MacOsX/ Windows
  • R package
  • Java 

:: DOWNLOAD

 FishingCNV

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jun 1;29(11):1461-2. doi: 10.1093/bioinformatics/btt151. Epub 2013 Mar 28.
FishingCNV: a graphical software package for detecting rare copy number variations in exome-sequencing data.
Shi Y1, Majewski J.

PATTERNCNV 1.0 – Detecting Copy Number changes from Exome Sequencing data

PATTERNCNV 1.0

:: DESCRIPTION

PatternCNV is a versatile tool to facilitate CNV detection and interpretation from either Germline or Tumor/Normal pairs of Exome-seq samples. “Pattern” stands for common trends summarized from Exome-seq data.

::DEVELOPER

Bioinformatics Program, Division of Biomedical Statistics and Informatics, Mayo Clinic Research

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • R package
  • Perl

:: DOWNLOAD

  PATTERNCNV 

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 29. pii: btu363. [Epub ahead of print]
PatternCNV: a versatile tool for detecting copy number changes from exome sequencing data.
Wang C1, Evans JM2, Bhagwate AV2, Prodduturi N2, Sarangi V2, Middha M2, Sicotte H2, Vedell PT2, Hart SN2, Oliver GR2, Kocher JP2, Maurer MJ2, Novak AJ2, Slager SL2, Cerhan JR2, Asmann YW

ExomeCopy 1.32.0 – Copy Number Variant Detection from Exome Sequencing Read Depth

ExomeCopy 1.32.0

:: DESCRIPTION

ExomeCopy implements a hidden Markov model which uses positional covariates, such as background read depth and GC-content, to simultaneously normalize and segment the samples into regions of constant copy count.

::DEVELOPER

Department Computational Molecular Biology, Max-Planck-Institute for Molecular Genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 ExomeCopy

:: MORE INFORMATION

Citation

Stat Appl Genet Mol Biol. 2011 Nov 8;10(1).
Modeling read counts for CNV detection in exome sequencing data.
Love MI, Myšičková A, Sun R, Kalscheuer V, Vingron M, Haas SA.