rapmad – Robust Analysis of Peptide MicroArray Data

rapmad

:: DESCRIPTION

rapmad is an R-package for the Robust Analysis of Peptide MicroArray Data. It is an automated, multi-step approach that combines several computational and statistical procedures to improve the quality of peptide microarray data and thus enable a more reliable analysis.

::DEVELOPER

The Institute for Translational Oncology and Immunology (TrOn)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux /MacOsX
  • R package

:: DOWNLOAD

   rapmad

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Aug 4;12:324. doi: 10.1186/1471-2105-12-324.
rapmad: Robust analysis of peptide microarray data.
Renard BY, Löwer M, Kühne Y, Reimer U, Rothermel A, Türeci O, Castle JC, Sahin U.

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.

SNPTools 1.0 – SNP analysis in Next Generation Sequencing data

SNPTools 1.0

:: DESCRIPTION

SNPTools is a suite of tools that enables integrative SNP analysis in next generation sequencing data with large cohorts. It not only calls SNP in a population with high sensitivity and accuracy, but also employs a novel imputation engine to achieve highly accurate genotype calls in an efficient way.

::DEVELOPER

Human Genome Sequencing Center, Baylor College of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler

:: DOWNLOAD

 SNPTools

:: MORE INFORMATION

Citation

Genome Res. 2013 Jan 7. [Epub ahead of print]
An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data.
Wang Y, Lu J, Yu J, Gibbs RA, Yu F.

PoPoolation 1.2.2 / PoPoolation2 1.201 / PoPoolation TE 1.02 – Analyse Pooled Next Generation Sequencing data

popoolation 1.2.2 / PoPoolation2 1.201 / PoPoolation TE 1.02

:: DESCRIPTION

PoPoolation is a collection of tools to facilitate population genetic studies of next generation sequencing data from pooled individuals

PoPoolation2 allows to compare allele frequencies for SNPs between two or more populations and to identify significant differences.

PoPoolation TE is a quick and simple pipeline for the analysis of transposable element insertions in (natural) populations using next generation sequencing.

DEVELOPER

Institute of Population Genetics, University of Veterinary Medicine Vienna

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 popoolation , PoPoolation2

:: MORE INFORMATION

Citation:

PoPoolation: a toolbox for population genetic analysis of next generation sequencing data from pooled individuals.
Kofler R, Orozco-terWengel P, De Maio N, Pandey RV, Nolte V, Futschik A, Kosiol C, Schlštterer C.
PLoS One. 2011 Jan 6;6(1):e15925.

Kofler,R.,Vinay Pandey, R. & Schloetterer, C
PoPoolation2: Identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq);
Bioinformatics; Vol. 27 no. 24 2011, pages 3435–3436; doi:10.1093/bioinformatics/btr589

Robert Kofler, Andrea Betancourt and Christian Schloetterer (2012):
Sequencing of Pooled DNA Samples (Pool-Seq) Uncovers Complex Dynamics of Transposable Element Insertions in Drosophila melanogaster;
PLoS Genet 8(1): e1002487. doi:10.1371/journal.pgen.1002487

MUFFINN – Cancer Gene Discovery via Network Analysis of Somatic Mutation data

MUFFINN

:: DESCRIPTION

MUFFINN (MUtations For Functional Impact on Network Neighbors) is a method for prioritizing cancer genes accounting for not only for mutations of individual genes but also those of neighbors in functional networks

::DEVELOPER

Network Biomedicine Laboratory at Yonsei University, Korea

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

MUFFINN

:: MORE INFORMATION

Citation

MUFFINN: cancer gene discovery via network analysis of somatic mutation data.
Cho A, Shim JE, Kim E, Supek F, Lehner B, Lee I.
Genome Biol. 2016 Jun 23;17(1):129. doi: 10.1186/s13059-016-0989-x.

BatMass 0.3.1 – Mass Spectrometry data Visualization

BatMass 0.3.1

:: DESCRIPTION

BatMass is a mass-spectrometry data visualization tool, with the main focus on being fast and interactive while providing comprehensive visualizations without any parameter tweaking.

::DEVELOPER

Proteomics & Integrative Bioinformatics Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOs
  • Java

:: DOWNLOAD

BatMass

:: MORE INFORMATION

Citation:

J Proteome Res. 2016 Aug 5;15(8):2500-9. doi: 10.1021/acs.jproteome.6b00021. Epub 2016 Jun 28.
BatMass: a Java Software Platform for LC-MS Data Visualization in Proteomics and Metabolomics.
Avtonomov DM, Raskind A, Nesvizhskii AI.

HapSeq 2 – Genotype Calling and Phasing for WGS data

HapSeq 2

:: DESCRIPTION

HapSeq2 is a program for genotyping calling and haplotype phasing from next generation sequencing data using haplotype information from jumping reads. Previously, we developed a Hidden Markov Model (HMM) based method for genotype calling and haplotype phasing from next generation data that can take into account jumping reads information across two adjacent potential polymorphic sites.

::DEVELOPER

ZhiGroup

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Window/Linux

:: DOWNLOAD

 HapSeq2

:: MORE INFORMATION

Citation:

Bioinformatics. 2012 Apr 1;28(7):938-46. doi: 10.1093/bioinformatics/bts047. Epub 2012 Jan 27.
Genotype calling from next-generation sequencing data using haplotype information of reads.
Zhi D, Wu J, Liu N, Zhang K.

ChromatoGate 1.2 – Analyze / Edit Chromatogram data

ChromatoGate 1.2

:: DESCRIPTION

ChromatoGate (CG) has been created to accelerate the process of detecting possible errors in DNA sequences that have been introduced by Sanger sequencers. To detect possible errors in the sequences, CG starts from the multiple-sequence alignment instead of inspecting every sequence separately.

::DEVELOPER

the Exelixis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 ChromatoGate

:: MORE INFORMATION

Citation

ChromatoGate: A Tool for Detecting Base Mis-Calls in Multiple Sequence Alignments by Semi-Automatic Chromatogram Inspection
Nikolaos Alachiotis, Emmanouella Vogiatzi, Pavlos Pavlidis, Alexandros Stamatakis
7th conference of the Hellenic Society for Computational Biology and Bioinformatics Volume No: 6, Issue: 7, March 2013, e201303001,

HiTEC 20110131 – Accurate Error Correction in High-throughput Sequencing data

HiTEC 20110131

:: DESCRIPTION

HiTEC (High Throughput Error Correction) , an algorithm that provides a highly accurate, robust and fully automated method to correct reads produced by high-throughput sequencing methods. The approach provides significantly higher accuracy than previous methods. It is time and space efficient and works very well for all read lengths, genome sizes and coverage levels.

::DEVELOPER

LUCIAN ILIE

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 HiTEC

:: MORE INFORMATION

Citation

L. Ilie, F. Fazayeli, S. Ilie,
HiTEC: accurate error correction in high-throughput sequencing data,
Bioinformatics 27(3) (2011) 295 — 302.

NGC 0.0.1 – Compressor for High-throughput Sequencing data

NGC 0.0.1

:: DESCRIPTION

NGC is a compressor for aligned HTS sequencing data that enables the complete lossless and lossy compression of mapped alignment data stored in SAM/BAM files.

::DEVELOPER

Niko Popitsch the Center of Integrative Bioinformatics Vienna (CIBIV)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 NGC

:: MORE INFORMATION

Citation

Niko Popitsch and Arndt von Haeseler
NGC: lossless and lossy compression of aligned high-throughput sequencing data
Nucl. Acids Res. (7 January 2013) 41 (1): e27.