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.

dbcAmplicons 0.6.7 – Analysis of Double Barcoded Illumina Amplicon Data

dbcAmplicons 0.6.7

:: DESCRIPTION

dbcAmplicons is a python application for processing massively multiplexed Illumina amplicon runs.

::DEVELOPER

Matt Settles

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows/ MacOsX
  • Python

:: DOWNLOAD

 dbcAmplicons

:: MORE INFORMATION

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.

SolexaQA 3.1.4 – Quality Assessment of Illumina Second-generation Sequencing data

SolexaQA 3.1.4

:: 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

Associate 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

Illuminate 0.6.2 – Analytics toolkit in Python for Illumina HiSeq and MiSeq metrics

Illuminate 0.6.2

:: DESCRIPTION

Illuminate parses the metrics binaries that result from Illumina sequencer runs, and provides usable data in the form of python dictionaries and dataframes. Intended to emulate the output of Illumina SAV, illuminate allows you to print sequencing run metrics to the command line as well as work with the data programmatically.

::DEVELOPER

Naomi Most , InVitae

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • Python

:: DOWNLOAD

 Illuminate

:: MORE INFORMATION

GenomeStudio 20151207 – Visualize and Analyze data generated by all of Illumina’s platform

GenomeStudio 20151207

:: DESCRIPTION

GenomeStudio is a software to visualize and analyze data generated by all of Illumina’s platform.This powerful informatics solution supports the primary analysis of sequence-based data produced by the Genome AnalyzerIIx and microarray-based data generated by the iScan System. Performance optimized tools and a user-friendly graphical interface allow you to quickly and easily convert data into meaningful results for your genome analysis and research.

::DEVELOPER

Illumina

:: SCREENSHOTS

GenomeStudio

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 GenomeStudio

:: MORE INFORMATION

Citation

Methods Mol Biol. 2011;784:77-98. doi: 10.1007/978-1-61779-289-2_6.
Gene expression profiling in formalin-fixed, paraffin-embedded tissues using the whole-genome DASL assay.
April CS, Fan JB.

FermiKit 0.13 – De novo Assembly based Variant Calling pipeline for Illumina Short Reads

FermiKit 0.13

:: DESCRIPTION

FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data.

::DEVELOPER

Heng Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 FermiKit

:: MORE INFORMATION

Citation

FermiKit: assembly-based variant calling for Illumina resequencing data.
Li H.
Bioinformatics. 2015 Nov 15;31(22):3694-6. doi: 10.1093/bioinformatics/btv440.