VirVarSeq – a low frequency Virus Variant detection pipeline for Illumina data

VirVarSeq

:: DESCRIPTION

VirVarSeq is a toolset designed to call variants at codon level in viral populations from deep sequencing data.

::DEVELOPER

VirTools team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

VirVarSeq

:: MORE INFORMATION

Citation

VirVarSeq: a low frequency Virus Variant detection pipeline for Illumina Sequencing using adaptive base-calling accuracy filtering.
Verbist BM, Thys K, Reumers J, Wetzels Y, Van der Borght K, Talloen W, Aerssens J, Clement L, Thas O.
Bioinformatics. 2014 Aug 31. pii: btu587.

snpQC – Quality Control of Illumina SNP Genotyping Array data

snpQC

:: DESCRIPTION

snpQC is an R based fully automated pipeline for preprocessing, storage and quality control of Illumina SNP data.

::DEVELOPER

Cedric Gondro

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Linux / MacOsX/ Windows
R

:: DOWNLOAD

snpQC

:: MORE INFORMATION

Citation

Anim Genet. 2014 Oct;45(5):758-61. doi: 10.1111/age.12198. Epub 2014 Jul 18.
SNPQC–an R pipeline for quality control of Illumina SNP genotyping array data.
Gondro C1, Porto-Neto LR, Lee SH.

TranscriptSimulator 0.7 – Simulate Transcriptome Next-gen Reads, including 454 and Illumina

TranscriptSimulator 0.7

:: DESCRIPTION

TranscriptSimulator: Simple text-based, next-gen output simulator. Specifically designed to simulate transcriptome next-gen reads, including 454 and Illumina. Uses a model to simulate transcription followed by simulated sequencing using various customizable parameters. Uses a nucleotide gene set as a template (e.g. in silico predicted gene set). Version 0.70 has simulated SNPs/Indels with an improved model.

::DEVELOPER

J. Cris Vera

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows

:: DOWNLOAD

TranscriptSimulator

:: MORE INFORMATION

NxTrim 0.4.3 – Optimized Trimming of Illumina Mate Pair Reads

NxTrim 0.4.3

:: DESCRIPTION

nxtrim: Software to remove Nextera Mate Pair adapters and categorise reads according to the orientation implied by the adapter location.

::DEVELOPER

Illumina

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
BOOST

:: DOWNLOAD

NxTrim

:: MORE INFORMATION

Citation

NxTrim: optimized trimming of Illumina mate pair reads.
O’Connell J, Schulz-Trieglaff O, Carlson E, Hims MM, Gormley NA, Cox AJ.
Bioinformatics. 2015 Feb 5. pii: btv057

illuminaio 0.34.0 – Parsing Illumina Microarray Output Files

illuminaio 0.34.0

:: DESCRIPTION

illuminaio is a suit of tools for parsing Illuminas microarray output files, including IDAT.

::DEVELOPER

Hansen Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
R
BioCOnductor

:: DOWNLOAD

illuminaio

:: MORE INFORMATION

Citation

F1000Res. 2013 Dec 4;2:264. doi: 10.12688/f1000research.2-264.v1. eCollection 2013.
illuminaio: An open source IDAT parsing tool for Illumina microarrays.
Smith ML, Baggerly KA, Bengtsson H, Ritchie ME, Hansen KD

Minfi 1.38.0 – Analyze Illumina’s 450k Methylation Arrays

Minfi 1.38.0

:: DESCRIPTION

Minfi is a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays.

::DEVELOPER

Hansen Lab

:: REQUIREMENTS

Linux / Windows/ MacOsX
R
BioCOnductor

:: DOWNLOAD

Minfi

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 15;30(10):1363-9. doi: 10.1093/bioinformatics/btu049. Epub 2014 Jan 28.
Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays.
Aryee MJ1, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, Irizarry RA.

illumina 1.0.6 – Preprocessing Illumina Whole Genome Expression BeadChips

illumina 1.0.6

:: DESCRIPTION

illumina is an R Library for preprocessing Illumina Whole Genome Expression BeadChips.

::DEVELOPER

WEHI Bioinformatics

:: SCREENSHOTS

N/a

:: REQUIREMENTS

Windows / Linux / MacOsX
R package

:: DOWNLOAD

illumina

:: MORE INFORMATION

Citation

Shi, W., Banerjee, A., Ritchie, M. E., Gerondakis, S., and Smyth, G. K.
Illumina WG-6 BeadChip strips should be normalized separately.
BMC Bioinformatics, 2009 Nov 11;10(1):372. [Epub ahead of print], PMID: 19903361

BIGpre 2.0.2 – Quality Assessment software for both Illumina and 454 platforms

BIGpre 2.0.2

:: DESCRIPTION

BIGpre is a quality assessment package for next-genomics sequencing data

::DEVELOPER

BIGpre team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

BIGpre

:: MORE INFORMATION

Citation

Genomics Proteomics Bioinformatics. 2011 Dec;9(6):238-44. doi: 10.1016/S1672-0229(11)60027-2.
BIGpre: a quality assessment package for next-generation sequencing data.
Zhang T1, Luo Y, Liu K, Pan L, Zhang B, Yu J, Hu S.

Bayexer – Demultiplexing Tool for Illumina sequencers

Bayexer

:: DESCRIPTION

Bayexer (Bayesian demultiplexing) is a fast and accurate tool for demultiplexing reads generated by Illumina sequencers.

::DEVELOPER

Haisi Yi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

Bayexer

:: MORE INFORMATION

Citation:

Bayexer: an accurate and fast Bayesian Demultiplexer for Illumina sequences.
Yi H, Li Z, Li T, Zhao J.
Bioinformatics. 2015 Aug 26. pii: btv501.

funtooNorm 1.00.1 – Normalization of Illumina Infinium Human Methylation 450 BeadChip

funtooNorm 1.00.1

:: DESCRIPTION

The R package funtooNorm provides a function for normalization of Illumina Infinium Human Methylation 450 BeadChip (Illumina 450K) data when there are samples from multiple tissues or cell types.

::DEVELOPER

Greenwood Lab, Statistical Genetics at the Lady Davis Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux/ MacOSX
R

:: DOWNLOAD

funtooNorm

:: MORE INFORMATION

Citation

funtooNorm: an R package for normalization of DNA methylation data when there are multiple cell or tissue types.
Oros Klein K, Grinek S, Bernatsky S, Bouchard L, Ciampi A, Colmegna I, Fortin JP, Gao L, Hivert MF, Hudson M, Kobor MS, Labbe A, MacIsaac JL, Meaney MJ, Morin AM, O’Donnell KJ, Pastinen T, Van Ijzendoorn MH, Voisin G, Greenwood CM.
Bioinformatics. 2015 Oct 24. pii: btv615.