Tag: Illumina

HumMeth27QCReport 1.2.14 – Quality Control of Illumina’s Infinium BeadChip Methylation Assays

HumMeth27QCReport 1.2.14

:: DESCRIPTION

HumMeth27QCReport is an R package that permits a quick overview of the quality of Illumina’s Infinium BeadChip methylation assays.

::DEVELOPER

Bioinformatics Core @ CRG

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX/Windows
  • R package
  • perl

:: DOWNLOAD

 HumMeth27QCReport

:: MORE INFORMATION

Citation

BMC Res Notes. 2011 Dec 19;4:546. doi: 10.1186/1756-0500-4-546.
HumMeth27QCReport: an R package for quality control and primary analysis of Illumina Infinium methylation data.
Mancuso FM, Montfort M, Carreras A, Alibés A, Roma G.

SToRM 0.0099 – Seed-based Read Mapping tool for SOLiD or Illumina sequencing data

SToRM 0.0099

:: DESCRIPTION

SToRM is a software tool primarily proposed for mapping SOLiD reads or Illumina reads to a reference genome. It was based on seeding techniques adapted to the statistical characteristics of the reads: the default seeds are for example designed (using the Iedera software) to comply with the properties of the SOLiD color encoding, or Illumina more classical encoding as well as the observed reading error distribution along the read.

::DEVELOPER

Bonsai Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  •  Linux / MacOsX
  • C Compiler

:: DOWNLOAD

 SToRM

:: MORE INFORMATION

Citation

Noé, L. and Gîrdea,. and Kucherov, G.:
Designing efficient spaced seeds for SOLiD read mapping
Advances in Bioinformatics, Volume 2010 2010

SolexaQA 3.1.7.1 – Quality Assessment of Illumina Second-generation Sequencing data

SolexaQA 3.1.7.1

:: DESCRIPTION

SolexaQA is a software package to calculate sequence quality statistics and create visual representations of data quality for Illumina’s second-generation sequencing technology (historically known as “Solexa”).

::DEVELOPER

Professor Murray Cox, Massey University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/
  • R package
  • Perl 

:: DOWNLOAD

 SolexaQA

:: MORE INFORMATION

Citation

Cox, M.P., D.A. Peterson, and P.J. Biggs. 2010.
SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data.
BMC Bioinformatics 11:485

Trowel 0.2.0.4 – Error Correction Module for Illumina Sequencing Reads

Trowel 0.2.0.4

:: DESCRIPTION

Trowel is an error correction module for Illumina sequencing reads, which is based on the k-mer spectrum approach. This tool is the first tool that uses a quality threshold instead of a coverage cutoff in order to extract trusted k-mers.

::DEVELOPER

Trowel team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • GCC

 Trowel

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Jul 29. pii: btu513.
Trowel: a fast and accurate error correction module for Illumina sequencing reads.
Lim EC, Müller J, Hagmann J, Henz SR, Kim ST, Weigel D.

InDelFixer 1.1 – An Insertion and Deletion Fixing Aligner for 454, Illumina and PacBio

InDelFixer 1.1

:: DESCRIPTION

InDelFixer is a java program to remove frame shift causing insertions or deletions from next-generation sequencing data.

::DEVELOPER

the Computational Biology Group (CBG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 InDelFixer

:: MORE INFORMATION

SHORE 0.9.3 – Analysis Suite for Illumina Short Read Data

SHORE 0.9.3

:: DESCRIPTION

SHORE is a mapping and analysis pipeline for short DNA sequences produced on Illumina Genome Analyzer and Hiseq 2000, Life Technology SOLiD, 454 Genome Sequencer FLX and PacBio RS platforms. It is designed for projects whose analysis strategy involves mapping of reads to a reference sequence. This reference sequence does not necessarily have to be from the same species, since weighted and gapped alignments allow for accuracy even in diverged regions. SHORE provides various prediction algorithms for genomic polymorphisms, i.e. SNPs, structural variants (indels, CNVs, unsequenced regions), SNPs and SV prediction in heterozygous or pooled samples, as well as peak detection for ChIP-Seq analysis and quantitative analysis of mRNA-Seq and sRNA-Seq.

::DEVELOPER

Dept. Weigel

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SHORE

:: MORE INFORMATION

Citation

Genome Res. 2008 Dec;18(12):2024-33. Epub 2008 Sep 25.
Sequencing of natural strains of Arabidopsis thaliana with short reads.
Ossowski S, Schneeberger K, Clark RM, Lanz C, Warthmann N, Weigel D.

RVboost 0.1 – RNA-seq Variant Prioritization approach for Illumina Next-generation Sequencing data

RVboost 0.1

:: DESCRIPTION

RVboost is a novel method specific for RNA variant prioritization.

::DEVELOPER

RVboost team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 RVboost

:: MORE INFORMATION

Citation

RVboost: RNA-Seq variants prioritization using a boosting method.
Wang C, Davila JI, Baheti S, Bhagwate AV, Wang X, Kocher JP, Slager SL, Feldman AL, Novak AJ, Cerhan JR, Thompson EA, Asmann YW.
Bioinformatics. 2014 Aug 27. pii: btu577

Mason 0.1.2 – Read Simulator software for Illumina, 454 and Sanger reads

Mason 0.1.2

:: DESCRIPTION

Mason is a read simulator software for Illumina, 454 and Sanger reads. Its features include position specific error rates and base quality values. For Illumina reads, we give a comprehensive analysis with empirical data for the error and quality model. For the other technologies, we use models from the literature. It has been written with performance in mind and can sample reads from large genomes.

::DEVELOPER

Manuel Holtgrewe

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX /Windows

:: DOWNLOAD

 Mason

:: MORE INFORMATION

Citation

Holtgrewe, M. (2010).
Mason – a read simulator for second generation sequencing data.
Technical Report TR-B-10-06, Institut für Mathematik und Informatik, Freie Universität Berlin.

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.

BayesCall 0.3 – Basecaller for the Illumina Platform

BayesCall 0.3

:: DESCRIPTION

BayesCall is a model-based basecalling algorithm for high-throughput short-read sequencing

::DEVELOPER

Yun S. Song

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 BayesCall

:: MORE INFORMATION

Citation

Kao, W.C., Stevens, K. and Song, Y.S.
BayesCall: A model-based basecalling algorithm for high-throughput short-read sequencing.
Genome Research, 19 (2009) 1884-1895.”