SNVMix2 – Detect Single Nucleotide Variants from Next Generation Sequencing

SNVMix2

:: DESCRIPTION

SNVMix is designed to detect single nucleotide variants from next generation sequencing data. SNVMix is a post-alignment tool. Given a pileup file (either Maq or Samtools format) as input and model parameters, SNVMix will output the probability that each position is one of three genotypes:  aa (homozygous for the reference allele, where the reference is the genome the reads were aligned to), ab (heterozygous) and bb (homozygous for a non-reference allele).  A tool for fitting the model using expectation maximization is also supplied (use -T option).

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SNVMix

:: MORE INFORMATION

Citation

Goya R, Sun MG, Morin RD, Leung G, Ha G, Wiegand KC, Senz J, Crisan A, Marra MA, Hirst M, Huntsman D, Murphy KP, Aparicio S, Shah SP.
SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors.
Bioinformatics. 2010 Mar 15;26(6):730-6.

USeq 9.2.3 – Analyze Next Generation Sequencing data from Illumina, SOLiD, and 454 platforms

USeq 9.2.3

:: DESCRIPTION

USeq is a collection of software tools for for both low and high level analysis of next generation, ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms. Initial emphasis: chIP-seq and RNA-Seq with FDR estimations.

::DEVELOPER

Huntsman Cancer Institute in the Utah Bioinformatics Shared Resource Center.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 USeq

:: MORE INFORMATION

Citation:

Nix DA, Courdy SJ, Boucher KM:
Empirical methods for controlling false positives and estimating confidence in chIP-seq peaks.
BMC Bioinformatics. 2008 Dec 5;9(1):523.

hapLOHseq 0.1.2 – Detection of Subtle Allelic Imbalance Events from Next-generation Sequencing data

hapLOHseq 0.1.2

:: DESCRIPTION

haplohseq identifies regions of allelic imbalance (AI) in sequencing data obtained from impure samples where AI events exist in a potentially low proportion of cells in the sample.

::DEVELOPER

paul scheet lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • R

:: DOWNLOAD

 hapLOHseq

:: MORE INFORMATION

Citation

Rapid and powerful detection of subtle allelic imbalance from exome sequencing data with hapLOHseq.
San Lucas FA, Sivakumar S, Vattathil S, Fowler J, Vilar E, Scheet P.
Bioinformatics. 2016 Jun 10. pii: btw340

MAFsnp 1.0 – SNP Caller Using Next-Generation Sequencing Data

MAFsnp 1.0

:: DESCRIPTION

MAFsnp (Multi-Sample Accurate and Flexible SNP Caller) is a SNP caller using next-generation sequencing data from multiple samples.

::DEVELOPER

Hong Zhang

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R

:: DOWNLOAD

MAFsnp

:: MORE INFORMATION

Citation

PLoS One. 2015 Aug 26;10(8):e0135332. doi: 10.1371/journal.pone.0135332. eCollection 2015.
MAFsnp: A Multi-Sample Accurate and Flexible SNP Caller Using Next-Generation Sequencing Data.
Hu J, Li T, Xiu Z, Zhang H

ebGenotyping 2.0.1 – Genotyping and SNP Detection using Next Generation Sequencing Data

ebGenotyping 2.0.1

:: DESCRIPTION

ebGenotyping is a novel statistical model to fit the observed non-reference allele frequency data, and utilize the empirical Bayes method for both genotyping and SNP detection, where an ECM algorithm is implemented to estimate the model parameters.

::DEVELOPER

Na You and Gongyi Huang <53hgy at 163.com>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows
  • R

:: DOWNLOAD

 ebGenotyping

:: MORE INFORMATION

Citation:

An Empirical Bayes Method for Genotyping and SNP Detection Using Multi-sample Next-generation Sequencing Data.
Huang G, Wang S, Wang X, You N.
Bioinformatics. 2016 Jul 4. pii: btw409.

QualiMap 2.2.1 – Evaluating Next Generation Sequencing Alignment data

QualiMap 2.2.1

:: DESCRIPTION

Qualimap is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data.

::DEVELOPER

QualiMap Team

:: SCREENSHOTS

QualiMap

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java
  • R package

:: DOWNLOAD

 Qualimap

:: MORE INFORMATION

Citation

Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data.
Okonechnikov K, Conesa A, García-Alcalde F.
Bioinformatics. 2015 Oct 1. pii: btv566

Bioinformatics. 2012 Oct 15;28(20):2678-9. doi: 10.1093/bioinformatics/bts503. Epub 2012 Aug 22.
Qualimap: evaluating next-generation sequencing alignment data.
García-Alcalde F, Okonechnikov K, Carbonell J, Cruz LM, Götz S, Tarazona S, Dopazo J, Meyer TF, Conesa A.

Skewer 0.2.1 – Adapter Trimmer for Next-generation Sequencing Paired-end Reads

Skewer 0.2.1

:: DESCRIPTION

Skewer implements a novel dynamic programming algorithm dedicated to the task of adapter trimming and it is specially designed for processing illumina paired-end sequences.

::DEVELOPER

Hongshan Jiang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Skewer

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Jun 12;15:182. doi: 10.1186/1471-2105-15-182.
Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads.
Jiang H, Lei R, Ding SW, Zhu S

MetaSV 0.5.3 – Structural-Variant caller for Next Generation Sequencing

MetaSV 0.5.3

:: DESCRIPTION

MetaSVM is an accurate method-aware merging algorithm for structural variations

::DEVELOPER

Bina Technologies

:: SCREENSHOTS

N/a

:: REQUIREMENTS

:: DOWNLOAD

 MetaSV

:: MORE INFORMATION

Citation

MetaSV: An accurate and integrative structural-variant caller for next generation sequencing.
Mohiyuddin M, Mu JC, Li J, Asadi NB, Gerstein MB, Abyzov A, Wong WH, Lam HY.
Bioinformatics. 2015 Apr 10. pii: btv204.

cn.MOPS 1.18.0 – Mixture Of PoissonS for Discovering Copy Number variations in Next Generation Sequencing data

cn.MOPS 1.18.0

:: DESCRIPTION

cn.MOPS is an algorithm that accurately detects copy number variations in next generation sequencing data in a study of multiple samples.

::DEVELOPER

Institute of Bioinformatics, Johannes Kepler University Linz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

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

:: DOWNLOAD

 cn.MOPS

:: MORE INFORMATION

Citation

Günter Klambauer, Karin Schwarzbauer, Andreas Mayr, Djork-Arné Clevert, Andreas Mitterecker, Ulrich Bodenhofer, Sepp Hochreiter.
cn.MOPS: mixture of Poissons for discovering copy number variations in next generation sequencing data with a low false discovery rate.
Nucleic Acids Research 2012 40(2)

ANGSD 0.911 – Analysis of Next Generation Sequencing Data

ANGSD 0.911

:: DESCRIPTION

ANGSD is a software for analyzing next generation sequencing data. The software can handle a number of different input types from mapped reads to imputed genotype probabilities. Most methods take genotype uncertainty into account instead of basing the analysis on called genotypes. This is especially useful for low and medium depth data.

::DEVELOPER

ANGSD team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 ANGSD

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Nov 25;15(1):356.
ANGSD: Analysis of Next Generation Sequencing Data.
Korneliussen T, Albrechtsen A, Nielsen R.