Tag: Exome

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.

ExomeCNV 1.4 – Exome Sequencing-based Copy-number Variation and Loss of Heterozygosity Detection

ExomeCNV 1.4

:: DESCRIPTION

ExomeCNV, a statistical method to detect CNV and LOH using depth-of-coverage and B-allele frequencies, from mapped short sequence reads.

::DEVELOPER

Nelsonlab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R package
  • Perl
  • Python
  • Samtool
  • GATK

:: DOWNLOAD

 ExomeCNV

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Oct 1;27(19):2648-54. doi: 10.1093/bioinformatics/btr462. Epub 2011 Aug 9.
Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV.
Sathirapongsasuti JF, Lee H, Horst BA, Brunner G, Cochran AJ, Binder S, Quackenbush J, Nelson SF.

Wessim 1.0 – Whole Exome Sequencing SIMulator using in silico exome capture

Wessim 1.0

:: DESCRIPTION

Wessim is a simulator for a targeted resequencing as generally known as exome sequencing. Wessim basically generates a set of artificial DNA fragments for next generation sequencing (NGS) read simulation.

::DEVELOPER

Sangwoo Kim

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • Python

:: DOWNLOAD

  Wessim

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Apr 15;29(8):1076-7. doi: 10.1093/bioinformatics/btt074. Epub 2013 Feb 14.
Wessim: a whole-exome sequencing simulator based on in silico exome capture.
Kim S, Jeong K, Bafna V.