vipR 0.0.16 – Variant Identification in pooled DNA using R

vipR 0.0.16

:: DESCRIPTION

vipR is a program to screen for sequence variants (SNPs, deletions) in sequence data generated by high-throughput-sequencing platforms.

::DEVELOPER

André Altmann

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

  vipR

:: MORE INFORMATION

Citation

vipR: variant identification in pooled DNA using R.
Altmann A, Weber P, Quast C, Rex-Haffner M, Binder EB, Müller-Myhsok B.
Bioinformatics. 2011 Jul 1;27(13):i77-84. doi: 10.1093/bioinformatics/btr205.

SERVIC4E – Effective Detection of Rare Variants in pooled DNA Samples

SERVIC4E

:: DESCRIPTION

SERVIC4E (Sensitive Rare Variant Identification by Cross-pool Cluster, Continuity, and tailCurve Evaluation) is a software program designed to identify SNPs from pooled sequencing data.

::DEVELOPER

Héctor Corrada Bravo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

 SERVIC4E

:: MORE INFORMATION

Citation:

Genome Biol. 2011 Sep 28;12(9):R93. doi: 10.1186/gb-2011-12-9-r93.
Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis.
Niranjan TS1, Adamczyk A, Bravo HC, Taub MA, Wheelan SJ, Irizarry R, Wang T.

SPLINTER – Identification of Indel Variants in Pooled DNA with Spike-in Controls

SPLINTER

:: DESCRIPTION

SPLINTER (Short IN/DEL Prediction by Large deviation Inference and Non-linear True frequency Estimation by Recursion) is a software which detects and quantifies short IN/DELs as well as single nucleotide substitutions in pooled-DNA samples. SPLINTER can accurately detect rare variants in large pools, providing a novel and sensitive method that will allow for significant progress in the discovery of novel disease-causing rare variants from DNA pools of affected individuals, such as germ-line mutation discovery for breast and ovarian cancer patients.

::DEVELOPER

Mitra Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SPLINTER

:: MORE INFORMATION

Citation:

Genome Res. 2010 Dec;20(12):1711-8. doi: 10.1101/gr.109157.110.
High-throughput discovery of rare insertions and deletions in large cohorts.
Vallania FL, Druley TE, Ramos E, Wang J, Borecki I, Province M, Mitra RD.

PDA 20060711 – Pooled DNA Analyzer

PDA 20060711

:: DESCRIPTION

PDA ( Pooled DNA analyzer ) is a powerful tool for analyses of pooled DNA data.

::DEVELOPER

Hsin-Chou Yang and Cathy SJ Fann(Institute of Biomedical Sciences, Academia Sinica, Taiwan)

:: SCREENSHOTS

::REQUIREMENTS

:: DOWNLOAD

 PDA

:: MORE INFORMATION

Citation

Hsin-Chou Yang, Chia-Ching Pan, Chin-Yu Lin and Cathy SJ Fann (2006).
PDA: pooled DNA analyzer.
BMC Bioinformatics, 7: 233.

PDA 2.0 – Pooled DNA Analyzer

PDA 2.0

:: DESCRIPTION

PDA, Pipeline Diversity Analysis, is a collection of programs and modules, mainly written in Perl, that automatically can:

explore for potentially polymorphic sequences from a large source of heterogeneous DNA,
extract and sort them out by gene, species and extent of similarity,
align the different groups, and
estimate the genetic diversity in different functional regions.

::DEVELOPER

Sònia Casillas and Antonio Barbadilla. Genomics, Bioinformatics and Evolution Group.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows
  • Perl

:: DOWNLOAD

  PDA

:: MORE INFORMATION

Citation

Sònia Casillas and Antonio Barbadilla (2006).
PDA v.2: improving the exploration and estimation of nucleotide polymorphism in large datasets of heterogeneous DNA.
Nucleic Acids Res. 34 (Web Server issue): W632-W634; doi: 10.1093/nar/gkl080

MPDA 20081110 – Microarray Pooled DNA Analyzer

MPDA 20081110

:: DESCRIPTION

MPDA (Microarray Pooled DNA Analyzer) is an innovative tool for analyzing hybridization intensity data from microarray-based pooled DNA experiments. Graphic and numerical outputs from MPDA support global and detailed inspection for bulk of genomic data.

::DEVELOPER

Hsin-Chou Yang and Cathy SJ Fann(Institute of Biomedical Sciences, Academia Sinica, Taiwan)

:: SCREENSHOTS

::REQUIREMENTS

:: DOWNLOAD

 MPDA

:: MORE INFORMATION

Citation

Hsin-Chou Yang, Mei-Chu Huang, Ling-Hui Li, Chien-Hsing Lin, Alice L. T. Yu, Mitchell B. Diccianni, Jer-Yuan Wu, Yuarn-Tsong Chen, Cathy S. J. Fann (2008).
MPDA: Microarray Pooled DNA Analyzer.
BMC Bioinformatics. 9:196.