DeNovoGear 1.1.1 – Detect denovo Mutations using Sequencing data of Related Individuals

DeNovoGear 1.1.1

:: DESCRIPTION

DeNovoGear is a program to detect denovo mutations using sequencing data.

::DEVELOPER

The Cartwright Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • Perl
  • C Compiler

:: DOWNLOAD

 DeNovoGear

:: MORE INFORMATION

Citation

Donald F Conrad et al.
Variation in genome-wide mutation rates within and between human families
Nature Genetics 43, 712–714 (2011) doi:10.1038/ng.862

SLICEMBLER – Meta-assembler Designed for Ultra-deep Sequencing data

SLICEMBLER

:: DESCRIPTION

SLICEMBLER is a meta-assembler designed for ultra-deep sequencing data

:: DEVELOPER

the algorithm and computational biology lab, university of California

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / windows/ MacOsX
  • Python

:: DOWNLOAD

 SLICEMBLER

:: MORE INFORMATION

Citation

De novo meta-assembly of ultra-deep sequencing data.
Mirebrahim H, Close TJ, Lonardi S.
Bioinformatics. 2015 Jun 15;31(12):i9-i16. doi: 10.1093/bioinformatics/btv226.

ePEST 1.0 – ChIP-exo Paired-ends Sequencing Processing Toolkit

ePEST 1.0

:: DESCRIPTION

ePEST leverages on the statistical powerful of r-scan for detecting binding peaks with son-3’-end reads and Chernoff inequality for identifying precise borders with exo-5′-end reads, respectively. The detected borders are further modelled as graphical components and classified into distinct border patterns based on their orientation and spacing.

::DEVELOPER

Jin Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ePEST

:: MORE INFORMATION

Citation

Ye Z, Chen Z, Sunkel B, Frietze S, Huang TH, Wang Q, Jin VX.
Genome-wide analysis reveals positional-nucleosome-oriented binding pattern of pioneer factor FOXA1.
Nucleic Acids Res. 2016 Sep 19;44(16):7540-54. doi: 10.1093/nar/gkw659. Epub 2016 Jul 25. PMID: 27458208; PMCID: PMC5027512.

DSS 2.40.0 – Dispersion Shrinakge for Sequencing data

DSS 2.40.0

:: DESCRIPTION

DSS is an R library performing differntial analysis for count-based sequencing data. It detectes differentially expressed genes (DEGs) from RNA-seq, and differentially methylated loci or regions (DML/DMRs) from bisulfite sequencing (BS-seq).

::DEVELOPER

Hao Wu, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /Linux/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

  DSS

:: MORE INFORMATION

Citation

Differential methylation analysis for BS-seq data under general experimental design.
Park Y, Wu H.
Bioinformatics. 2016 Jan 27. pii: btw026

Wu H, Wang C and Wu Z
A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data.
Biostat (2013) 14 (2): 232-243. http://dx.doi.org/10.1093/biostatistics/kxs033.

easym6A v1.0.0 – A pipeline for m6A Sequencing data pre-processing

easym6A v1.0.0

:: DESCRIPTION

easym6A creates a bash script to process m6A/MeRIP-seq data from adapter trimming to peak calling. It can also serve as a pipeline for RNA-seq data.

::DEVELOPER

Chen Group at U Chicago

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX

:: DOWNLOAD

easym6A

:: MORE INFORMATION

Citation

Liu S, Zhu A, He C, Chen M.
REPIC: a database for exploring the N6-methyladenosine methylome.
Genome Biol. 2020 Apr 28;21(1):100. doi: 10.1186/s13059-020-02012-4. PMID: 32345346; PMCID: PMC7187508.

MethylViewer 20120328 – Interactive data analysis of Bisulphite DNA Sequencing to Map Chromatin Structure using DNA Methyltransferases

MethylViewer 20120328

:: DESCRIPTION

MethylViewer was developed from CpGviewer such that the program can now analyse up to four different methylation sites such as CpG, GpC, CpNpG or any four user defined sites. If a non-native DNA methylase is used to modify chromatin-bound DNA, the methylation pattern can be used to identify the binding sites of DNA-binding proteins.

::DEVELOPER

Ian’s DNA@Leeds

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows
  • Microsoft .NET framework version 2.0 

:: DOWNLOAD

 MethylViewer

:: MORE INFORMATION

Citation

Pardo C, Carr IM, Hoffman C, Darst R, Markham AF, Bonthron DT, Kladde M
MethylViewer: computational analysis and editing for bisulphite sequencing and Methyltransferase Accessibility Protocol for Individual Templates (MAPit) projects.
Nucleic Acids Res. 2011 Jan 1;39(1):e5

ASAP 0.1.2 – Align a Sequencing to two Genomes at the Same Time

ASAP 0.1.2

:: DESCRIPTION

ASAP(Allele-specific Alignment Pipeline) is a program to align a sequencing file to two genomes at the same time. This can be useful to detect allelic imbalances in samples which are of different genetic origin. Examples would be studying imprinted regions in ChIP-Seq or RNA-Seq experiments, or genomic interactions (e4C) in mouse strains with a mixed genetic background.

:: DEVELOPER

Babraham Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 ASAP

:: MORE INFORMATION

MultiBreak-SV – Detect Structural Variants from Single Molecule Sequencing data

MultiBreak-SV

: DESCRIPTION

MultiBreak-SV is a software for structural variation analysis from next-generation paired end data, third-generation long read data, or data from a combination of sequencing platforms.

::DEVELOPER

Raphael Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Java

:: DOWNLOAD

 MultiBreak-SV

:: MORE INFORMATION

Citation:

Characterization of Structural Variants with Single Molecule and Hybrid Sequencing Approaches.
Ritz A, Bashir A, Sindi S, Hsu D, Hajirasouliha I, Raphael BJ.
Bioinformatics. 2014 Oct 28. pii: btu714.

ngs-bits 2021_03 – Short-read sequencing tools

ngs-bits 2021_03

:: DESCRIPTION

ngs-bits is a collection of tools for short-read data analysis.

::DEVELOPER

Arbeitsgruppe Genomik

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • Bioconda

:: DOWNLOAD

ngs-bits

:: MORE INFORMATION

Citation

Schroeder CM, Hilke FJ, Löffler MW, Bitzer M, Lenz F, Sturm M.
A comprehensive quality control workflow for paired tumor-normal NGS experiments.
Bioinformatics. 2017 Jun 1;33(11):1721-1722. doi: 10.1093/bioinformatics/btx032. PMID: 28130233.

GBStools – Bioinformatics tools for Reduced Representation Sequencing data

GBStools

:: DESCRIPTION

GBStools provides bioinformatics tools for genotyping-by-sequencing data, including allele frequency estimation at variant restriction sites.

:: DEVELOPER

the Bustamante Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

GBStools

:: MORE INFORMATION

Citation

Cooke TF, Yee MC, Muzzio M, Sockell A, Bell R, Cornejo OE, Kelley JL, Bailliet G, Bravi CM, Bustamante CD, Kenny EE.
GBStools: A Statistical Method for Estimating Allelic Dropout in Reduced Representation Sequencing Data.
PLoS Genet. 2016 Feb 1;12(2):e1005631. doi: 10.1371/journal.pgen.1005631. PMID: 26828719; PMCID: PMC4734769.