SVDetect 0.8b – Detect Genomic Structural Variations from Paired-end and Mate-pair Sequencing data

SVDetect 0.8b

:: DESCRIPTION

SVDetect is a application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies.

::DEVELOPER

Boeva lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SVDetect

:: MORE INFORMATION

Citation:

Bioinformatics. 2010 Aug 1;26(15):1895-6.
SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data.
Zeitouni B, Boeva V, Janoueix-Lerosey I, Loeillet S, Legoix-né P, Nicolas A, Delattre O, Barillot E.

Pyicoteo 2.0.7 – Analysis of High-throughput Sequencing data

Pyicoteo 2.0.7

:: DESCRIPTION

Pyicoteo is a suite of tools for the analysis of high-throughput sequencing data. It works with genomic coordinates, it was mainly developed using Solexa/Illumina mapped reads, but in its core it is platform-agnostic.

::DEVELOPER

Eyras Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Python

:: DOWNLOAD

 Pyicoteo

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Dec 15;27(24):3333-40. Epub 2011 Oct 12.
Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data.
Althammer S, González-Vallinas J, Ballaré C, Beato M, Eyras E.

SPP 1.13 – Analysis of Sequencing data from Chromatin Immunoprecipitation Experiments

SPP 1.11

:: DESCRIPTION

SPP is an R package by Peter Kharchenko implements tools for analysis of sequencing data from chromatin immunoprecipitation experiments. It includes normalization of the binding profile, detection of enriched regions, and an estimate of read depth needed to achieve saturation of binding sites.

::DEVELOPER

Peter Park’s lab at CBMI, Harvard Medical School

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SPP

:: MORE INFORMATION

Citation

Kharchenko PK, Tolstorukov MY, Park PJ
Design and analysis of ChIP-seq experiments for DNA-binding proteins
Nat. Biotech. doi:10.1038/nbt.1508

Mutascope 1.0.2 – Analysis software designed for PCR-amplicon Sequencing data

Mutascope 1.0.2

:: DESCRIPTION

Mutascope is a software suite designed to analyze data from high throughput sequencing of PCR amplicons, with an emphasis on normal-tumor comparison for the accurate and sensitive identification of low prevalence mutations.

::DEVELOPER

frazer Lab, UCSD

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • R package
  • MCLUST
  • SAMTools
  • BWA

:: DOWNLOAD

 Mutascope

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Aug 1;29(15):1908-9. doi: 10.1093/bioinformatics/btt305. Epub 2013 May 27.
Mutascope: sensitive detection of somatic mutations from deep amplicon sequencing.
Yost SE, Alakus H, Matsui H, Schwab RB, Jepsen K, Frazer KA, Harismendy O.

Reveel 201610 – Large-scale Population Genotyper using low-coverage Sequencing data

Reveel 201610

:: DESCRIPTION

Reveel is an ultrafast tool for single nucleotide variant calling and genotyping of large cohorts that have been sequenced at low coverage.

::DEVELOPER

Serafim’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Java

:: DOWNLOAD

 Reveel

:: MORE INFORMATION

Citation

Reveel: large-scale population genotyping using low-coverage sequencing data.
Huang L, Wang B, Chen R, Bercovici S, Batzoglou S.
Bioinformatics. 2015 Sep 9. pii: btv530.

ReportingTools 2.32.1 – Tools for Making Microarray and Sequencing Data Reports in various Formats

ReportingTools 2.32.1

:: DESCRIPTION

The ReportingTools software package enables users to easily display reports of analysis results generated from sources such as microarray and sequencing data. The package allows users to create HTML pages that may be viewed on a web browser such as Safari, or in other formats readable by programs such as Excel.

:: DEVELOPER

ReportingTools team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX/Windows
  • R package
  • BioConductor

:: DOWNLOAD

  ReportingTools

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Oct 18.
ReportingTools: an automated result processing and presentation toolkit for high-throughput genomic analyses.
Huntley MA, Larson JL, Chaivorapol C, Becker G, Lawrence M, Hackney JA, Kaminker JS.

CircTest 0.1.0 / DCC 0.5.0 – Identification and Quantification of Circular RNAs from Sequencing Data

CircTest 0.1.0 / DCC 0.5.0

:: DESCRIPTION

CircTest tests the variation of circRNAs in respect to host genes.

DCC (detect circRNAs from chimeric reads) is a python package intended to detect and quantify circRNAs with high specificity.

::DEVELOPER

Dieterich lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R
  • Python

:: DOWNLOAD

 CircTest , DCC

:: MORE INFORMATION

Citation

Specific identification and quantification of circular RNAs from sequencing data.
Cheng J, Metge F, Dieterich C.
Bioinformatics. 2015 Nov 9. pii: btv656

CAGEr 1.34.0 – Analysis of CAGE (Cap Analysis of Gene Expression) Sequencing Data

CAGEr 1.34.0

:: DESCRIPTION

CAGEr is an R implementation of novel methods for the analysis of differential TSS usage and promoter dynamics, integrated with CAGE data processing and promoterome mining into a first comprehensive CAGE toolbox on a common analysis platform.

::DEVELOPER

FANTOM

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 CAGEr

:: MORE INFORMATION

Citation

CAGEr: precise TSS data retrieval and high-resolution promoterome mining for integrative analyses.
Haberle V, Forrest AR, Hayashizaki Y, Carninci P, Lenhard B.
Nucleic Acids Res. 2015 Feb 4. pii: gkv054.

PerM 0.4.0 – Read-mapping software based on Periodic Spaced Seeds for both Illumina and SOLiD sequencing data

PerM 0.4.0

:: DESCRIPTION

PerM is a software package which was designed to perform highly efficient genome scale alignments for hundreds of millions of short reads produced by the ABI SOLiD and Illumina sequencing platforms. Today PerM is capable of providing full sensitivity for alignments within 4 mismatches for 50bp SOLID reads and 9 mismatches for 100bp Illumina reads.

::DEVELOPER

Ting Chen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

 PerM

:: MORE INFORMATION

Citation:

Yangho Chen, Tade Souaiaia and Ting Chen
PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds
Bioinformatics (2009) 25 (19): 2514-2521.

BitSeq 0.7.5 / for R 1.36.0 – Bayesian Inference of Transcripts from Sequencing Data

BitSeq 0.7.5 / for R 1.36.0

:: DESCRIPTION

BitSeq is an application for inferring expression levels of individual transcripts from sequencing (RNA-Seq) data and estimating differential expression (DE) between conditions. An advantage of this approach is the ability to account for both technical uncertainty and intrinsic biological variance in order to avoid false DE calls. The technical contribution to the uncertainty comes both from finite read-depth and the possibly ambiguous mapping of reads to multiple transcripts.

:: DEVELOPER

Peter Glaus , Antti Honkela

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / windows/ MacOsX
  • GCC / BioCOnductor/ R package
  • Python

:: DOWNLOAD

 BitSeq / for R

:: MORE INFORMATION

Citation

Fast and accurate approximate inference of transcript expression from RNA-seq data.
Hensman J, Papastamoulis P, Glaus P, Honkela A, Rattray M.
Bioinformatics. 2015 Aug 26. pii: btv483

Bioinformatics. 2012 Jul 1;28(13):1721-8. doi: 10.1093/bioinformatics/bts260. Epub 2012 May 3.
Identifying differentially expressed transcripts from RNA-seq data with biological variation.
Glaus P, Honkela A, Rattray M.

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