Tag: Detection

EM-SNP – Allele Frequency Estimation, SNP Detection and Association Studies

EM-SNP

:: DESCRIPTION

EM-SNP is an unified approach for allele frequency estimation, SNP detection and association studies based on pooled sequencing data using EM algorithms

::DEVELOPER

Fengzhu Sun

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • R

:: DOWNLOAD

  EM-SNP

:: MORE INFORMATION

Citation

Quan Chen and Fengzhu Sun (2013):
A unified approach for allele frequency estimation, SNP detection and association studies on pooled sequencing data using EM algorithms.
BMC Genomics. 2013;14 Suppl 1:S1. doi: 10.1186/1471-2164-14-S1-S1.

PASSion 1.2.1 – Pattern Growth algorithm based Pileline for Splice Site Detection in Paired-end RNA-Seq data

PASSion 1.2.1

:: DESCRIPTION

PASSion uses the mapped read in a pair as anchor and then uses a high resolution algorithm, pattern growth, to remap the proximal and distal fragments of the unmapped read to a local region of the reference indicated by the mate. It is capable of identifying both known and novel canonical and non-canonical junctions with SNP or sequencing error tolerance.

::DEVELOPER

Yanju Zhang (Leiden University Medical Center, The Netherlands): y.zhang AT lumc.nl

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PASSion

:: MORE INFORMATION

Citation:

PASSion: A Pattern Growth Algorithm Based Pipeline for Splice Junction Detection in Paired-end RNA-Seq Data
Yanju Zhang; Eric-Wubbo Lameijer; Peter A.C. ‘t Hoen; Zemin Ning; P. Eline Slagboom; Kai Ye
Bioinformatics 2012; doi: 10.1093/bioinformatics/btr712

REDItools 1.2.1 / REDItools2 – RNA editing detection by NGS data

REDItools 1.2.1 / REDItools2

:: DESCRIPTION

REDItools are python scripts developed with the aim to study RNA editing at genomic scale by next generation sequencing data.

REDItools2 is the optimized, parallel multi-node version of REDItools.

::DEVELOPER

Ernesto Picardi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 REDItools , REDItools2

:: MORE INFORMATION

Citation

Curr Protoc Bioinformatics. 2015 Mar 9;49:12.12.1-12.12.15. doi: 10.1002/0471250953.bi1212s49.
Using REDItools to Detect RNA Editing Events in NGS Datasets.
Picardi E1, D’Erchia AM, Montalvo A, Pesole G.

VDJSeq-Solver – in Silico VDJ Recombination Detection tool

VDJSeq-Solver

:: DESCRIPTION

VDJSeq-Solver is a completely automated workflow for the in silico detection of the main clone V(D)J recombination sequence characterizing neoplastic tissues, using RNA-Seq paired-end reads.

::DEVELOPER

EDA (Electronic Design Automation Group)

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • TopHat
  • Java
  • Perl
  • BEDTools
  • Bowtie
  • Blast
  • SHRiMP
  • Samtools

:: DOWNLOAD

 VDJSeq-Solver

:: MORE INFORMATION

Citation

VDJSeq-Solver: In Silico V(D)J Recombination Detection Tool.
Paciello G, Acquaviva A, Pighi C, Ferrarini A, Macii E, Zamo’ A, Ficarra E.
PLoS One. 2015 Mar 23;10(3):e0118192. doi: 10.1371/journal.pone.0118192.

IDP 0.1.10/ IDP-fusion v1.1.2 – Gene Isoform Detection and Prediction tool

IDP 0.1.10 / IDP-fusion v1.1.2

:: DESCRIPTION

IDP is an gene Isoform Detection and Prediction tool from Second Generation Sequencing and PacBio sequencing. It offers very reliable gene isoform identification with high sensitivity.

IDP-fusion is an gene Isoform Detection and Prediction tool from Second Generation Sequencing and PacBio sequencing.

::DEVELOPER

Au Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOSX
  • Python

:: DOWNLOAD

 IDP / IDP-fusion

:: MORE INFORMATION

Citation

Weirather JL, Afshar PT, Clark TA, Tseng E, Powers LS, Underwood JG, Zabner J, Korlach J, Wong WH, Au KF.
Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing.
Nucleic Acids Res. 2015 Oct 15;43(18):e116. doi: 10.1093/nar/gkv562. Epub 2015 Jun 3. PMID: 26040699; PMCID: PMC4605286.

Kin Fai Au, Vittorio Sebastiano, Pegah Tootoonchi Afshar, Jens Durruthy Durruthy, Lawrence Lee, Brian A. Williams, Honoratus Van Bakel, Eric Schadt, Renee A. Reijo Pera, Jason Underwood, Wing Hung Wong
Characterization of the human ESC transcriptome by hybrid sequencing
Proc. Natl. Acad. Sci. USA 2013 110 (50) E4821-E4830

NGS-eval – NGS Error Analysis and VAriant Detection tooL

NGS-eval

:: DESCRIPTION

NGS-eval is an interactive web server for error analysis and sequence variant detection in amplicon-based NGS mock (or marker gene) data sets.

::DEVELOPER

The Centre for Integrative Bioinformatics VU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

NGS-eval: NGS Error analysis and novel sequence VAriant detection tooL.
May A, Abeln S, Buijs MJ, Heringa J, Crielaard W, Brandt BW.
Nucleic Acids Res. 2015 Apr 15. pii: gkv346.

CATCh v1 – Ensemble Classifier for Chimera Detection in 16S rRNA Sequencing Studies

CATCh v1

:: DESCRIPTION

CATCh is an ensemble classifier for chimera detection in 16S rRNA sequencing studies

::DEVELOPER

The Bioinformatics team of the Microbiology Unit, SCK.CEN

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 CATCh

:: MORE INFORMATION

Citation

Appl Environ Microbiol. 2015 Mar;81(5):1573-84. doi: 10.1128/AEM.02896-14. Epub 2014 Dec 19.
CATCh, an ensemble classifier for chimera detection in 16S rRNA sequencing studies.
Mysara M, Saeys Y, Leys N, Raes J, Monsieurs P

intcomp 0.3.30 – integrative Cancer Gene Detection algorithms

intcomp 0.3.30

:: DESCRIPTION

The intcomp R package provides a benchmarking tools for quantitative comparison of cancer gene detection algorithms based on integrative analysis of DNA copy number and gene expression data.

::DEVELOPER

Turku Data Science Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R package

:: DOWNLOAD

  intcomp

:: MORE INFORMATION

Citation

Brief Bioinform. 2013 Jan;14(1):27-35. doi: 10.1093/bib/bbs005. Epub 2012 Mar 22.
Cancer gene prioritization by integrative analysis of mRNA expression and DNA copy number data: a comparative review.
Lahti L, Schäfer M, Klein HU, Bicciato S, Dugas M.

UVPAR – Fast Detection of Functional Shifts in Duplicate Genes

UVPAR

:: DESCRIPTION

UVPAR is a program designed to quickly test for changes in the functional constraints of duplicate genes.

::DEVELOPER

Bioinformatics Unit, Instituto de Biomedicina de Valencia (CSIC) / Universidad de Valencia

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Windows/Linux

:: DOWNLOAD

 UVPAR

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2006 Mar 28;7:174.
UVPAR: fast detection of functional shifts in duplicate genes.
Arnau V1, Gallach M, Lucas JI, Marín I.

NovelSeq 1.0.2 – Novel Sequence Insertions Detection

NovelSeq 1.0.2

:: DESCRIPTION

NovelSeq is a computational framework to discover the content and location of long novel sequence insertions using paired-end sequencing data generated by the next-generation sequencing platforms. Our framework can be built as part of a general sequence analysis pipeline to discover multiple types of genetic variation (SNPs, structural variation, etc.), thus it requires significantly less-computational resources than de novo sequence assembly. We apply our methods to detect novel sequence insertions in the genome of an anonymous donor and validate our results by comparing with the insertions discovered in the same genome using various sources of sequence data.

::DEVELOPER

Lab for Bioinformatics and Computational Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • C Complier

:: DOWNLOAD

 NovelSeq

:: MORE INFORMATION

Detection and characterization of novel sequence insertions using paired-end next-generation sequencing
Iman Hajirasouliha, Fereydoun Hormozdiari, Can Alkan, Jeffrey M. Kidd, Inanc Birol, Evan E. Eichler, S. Cenk Sahinalp
Bioinformatics 2010 26(10):1277-1283