Tag: Next Generation Sequencing

r3Cseq 1.38.0 – Discovery of Long-range Genomic Interactions from Chromosome Conformation Capture and Next-generation Sequencing data

r3Cseq 1.38.0

:: DESCRIPTION

r3Cseq is an R package designed to identify chromosomal interaction regions generated by chromosome conformation capture (3C) coupled to next-generation sequencing (NGS), a technique termed 3C-seq. r3Cseq was designed to perform data analysis for a number of different experimental designs, as it can analyze 3C-seq data with or without a control experiment and it can be used to facilitate data analysis for experiments with multiple replicates. The r3Cseq package provides functions to perform data normalization, statistical analysis for cis/trans interactions and visualization in order to help scientists identify genomic regions that physically interact with the given viewpoints of interest. This tool greatly facilitates hypothesis generation and the interpretation of experimental results.

::DEVELOPER

Supat Thongjuea 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Mac OsX / Windows
  • R package

:: DOWNLOAD

 r3Cseq

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jul;41(13):e132. doi: 10.1093/nar/gkt373. Epub 2013 May 13.
r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data.
Thongjuea S, Stadhouders R, Grosveld FG, Soler E, Lenhard B.

BM-Map 2.0.1 – Refining Next-Generation Sequencing (NGS) Read Mapping

BM-Map 2.0.1

:: DESCRIPTION

BM-Map is a powerful NGS genomic loci mapping refiner. It improves the mapping of the multireads (reads mapped to more than one genomic location with similar fidelities), as a refinement step after the general read-alignment is completed.

::DEVELOPER

Yuan Ji Lab  and Dr. Han Liang’s group.

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX

:: DOWNLOAD

 BM-Map

:: MORE INFORMATION

Citation

BMC Genomics. 2012;13 Suppl 8:S9. doi: 10.1186/1471-2164-13-S8-S9. Epub 2012 Dec 17.
BM-Map: an efficient software package for accurately allocating multireads of RNA-sequencing data.
Yuan Y1, Norris C, Xu Y, Tsui KW, Ji Y, Liang H.

Biometrics. 2011 Dec;67(4):1215-24. doi: 10.1111/j.1541-0420.2011.01605.x. Epub 2011 Apr 22.
BM-map: Bayesian mapping of multireads for next-generation sequencing data.
Ji Y, Xu Y, Zhang Q, Tsui KW, Yuan Y, Norris C Jr, Liang S, Liang H.

ngSeqUtils 1.2.1 – Utility Scripts in Python for Handling Next Generation Sequencing data

ngSeqUtils 1.2.1

:: DESCRIPTION

ngSeqUtils is a small collection of scripts to assist data analysis of Next Generation Sequencing data and handle wig, bigwig, and gff files in python.

::DEVELOPER

The Barton Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Python

:: DOWNLOAD

 ngSeqUtils

 :: MORE INFORMATION

PSE-HMM v1 – Genome-wide CNV detection from Next Generation Sequencing data

PSE-HMM v1

:: DESCRIPTION

PSE-HMM is a tool for the genome-wide CNV detection from Next Generation Sequencing data (mate pair reads). PSE-HMM applies an HMM with Position-Specific Emission probabilities for modeling different aberrations in the mate pairs, after being mapped to the reference genome.

::DEVELOPER

School of Biological Sciences, Iran

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX
  • MatLab

:: DOWNLOAD

PSE-HMM

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2016 Nov 3;18(1):30. doi: 10.1186/s12859-016-1296-y.
PSE-HMM: genome-wide CNV detection from NGS data using an HMM with Position-Specific Emission probabilities.
Malekpour SA, Pezeshk H, Sadeghi M

glfMultiples 20100616 – GLF-based Variant Caller for Next-generation Sequencing data

glfMultiples 20100616

:: DESCRIPTION

glfMultiples is a GLF-based variant caller for next-generation sequencing data. It takes a set of GLF format genotype likelihood files as input and generates a VCF-format set of variant calls as output

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 glfMultiples

:: MORE INFORMATION

AYB 2.11 – Advanced Base Calling for Next Generation Sequencing Machines

AYB 2.11

:: DESCRIPTION

AYB (All your base) is a base caller for the Illumina Genome Analyzer, using an explicit statistical model of how errors occur during sequencing to produce more accurate reads from the raw intensity data.

::DEVELOPER

Goldman Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 AYB

:: MORE INFORMATION

Citation:

Genome Biol. 2012 Feb 29;13(2):R13. [Epub ahead of print]
All your base: a fast and accurate probabilistic approach to base calling.
Massingham T, Goldman N.

Olorin 1.0.1 – Interactive Filtering tool for Next Generation Sequencing data

Olorin 1.0.1

:: DESCRIPTION

Olorin is an interactive filtering tool for next generation sequencing data coming from the study of large complex disease pedigrees.

::DEVELOPER

Olorin team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Java

:: DOWNLOAD

 Olorin

:: MORE INFORMATION

Citation

Olorin: combining gene flow with exome sequencing in large family studies of complex disease.
Morris JA and Barrett JC
Bioinformatics (Oxford, England) 2012;28;24;3320-1

NGSTools 2.0.0 – Analysis of Next Generation Sequencing (NGS) data

NGSTools 2.0.0

:: DESCRIPTION

NGSTools package provides an object model to enable different types of analyses of Next Generation Sequencing (NGS) data, and some utility programs to process reads aligned to different reference genomes. The most important tools in this package are SNVQ, an accurate Single Nucleotide Variants (SNV) detection and genotyping algorithm from base calls and quality scores and a rule set to merge read alignments to a CCDS transcripts library with alignments of the same reads to a reference assembly.

::DEVELOPER

Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

NGSTools

:: MORE INFORMATION

Citation:

J. Duitama and P.K. Srivastava and I.I. Mandoiu,
Towards Accurate Detection and Genotyping of Expressed Variants fromWhole Transcriptome Sequencing Data
Proc. 1st IEEE International Conference on Computational Advances in Bio and Medical Sciences, pp. 87-92, 201

EBVariant 1.0 – An Empirical Bayes Testing Procedure for Variants Detection in Next Generation Sequencing

EBVariant 1.0

:: DESCRIPTION

EBVariant is an optimal empirical Bayes testing procedure to detect variants for NGS study. It exploits the across-site information among vast amount of testing sites in Next Generation Sequencing data, and thus, comparing to conventional Bayesian models or frequestist tests, EBVariant is able to address the multiplicity and testing efficiency issues simultaneously.

:: SCREENSHOTS

N/A

::DEVELOPER

Zhi Wei

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • R package/Java

:: DOWNLOAD

 EBVariant

:: MORE INFORMATION

Citation

Zhao Z, Wang W, and Wei Z.
An empirical Bayes testing procedure for detecting variants in analysis of next generation sequencing data.
Annals of Applied Statistics, accepted.

Galaxy LIMS – LIMS for Next-generation Sequencing

Galaxy LIMS

:: DESCRIPTION

Galaxy LIMS is a laboratory information management system (LIMS) for a next-generation sequencing (NGS) laboratory within the existing Galaxy platform. The system provides lab technicians standard and customizable sample information forms, barcoded submission forms, tracking of input sample quality, multiplex-capable automatic flow cell design and automatically generated sample sheets to aid physical flow cell preparation.

::DEVELOPER

The Institute for Translational Oncology and Immunology(TrOn)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Galaxy LIMS

:: MORE INFORMATION

Citation

Bioinformatics. 2013 May 1;29(9):1233-4. doi: 10.1093/bioinformatics/btt115. Epub 2013 Mar 11.
Galaxy LIMS for next-generation sequencing.
Scholtalbers J, Rößler J, Sorn P, de Graaf J, Boisguérin V, Castle J, Sahin U.