miRlastic 1.0 – Integrative Analysis of miRNA and mRNA Expression data

miRlastic 1.0

:: DESCRIPTION

miRlastic is a novel method  which infers miRNA-target interactions using transcriptomic data as well as prior knowledge and performs functional annotation of target genes by exploiting the local structure of the inferred network.

::DEVELOPER

Computational Cell Maps Group

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Windows/ Linux
  • R

:: DOWNLOAD

 miRlastic

:: MORE INFORMATION

Citation

MicroRNA-Target Network Inference and Local Network Enrichment Analysis Identify Two microRNA Clusters with Distinct Functions in Head and Neck Squamous Cell Carcinoma.
Sass S, Pitea A, Unger K, Hess J, Mueller NS, Theis FJ.
Int J Mol Sci. 2015 Dec 18;16(12):30204-22. doi: 10.3390/ijms161226230.

FASTX-Toolkit 0.0.14 – Short-Reads FASTA/FASTQ files Preprocessing

FASTX-Toolkit 0.0.14

:: DESCRIPTION

The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.The main processing of such FASTA/FASTQ files is mapping (aka aligning) the sequences to reference genomes or other databases using specialized programs.However,It is sometimes more productive to preprocess the FASTA/FASTQ files before mapping the sequences to the genome – manipulating the sequences to produce better mapping results.The FASTX-Toolkit tools perform some of these preprocessing tasks.

:: DEVELOPER

The Hannon laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  FASTX-Toolkit

:: MORE INFORMATION

mtDNA-Server v2 – Analysis of human Mitochondrial DNA data

mtDNA-Server v2

:: DESCRIPTION

mtDNA-Server is a free mtDNA NGS analysis pipeline including heteroplasmy detection and haplogroup-based contamination deconvolution.

::DEVELOPER

GenEpi – Division of Genetic Epidemiology Innsbruck

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

mtDNA-Server: next-generation sequencing data analysis of human mitochondrial DNA in the cloud.
Weissensteiner H, Forer L, Fuchsberger C, Schöpf B, Kloss-Brandstätter A, Specht G, Kronenberg F, Schönherr S.
Nucleic Acids Res. 2016 Apr 15. pii: gkw247

cutadapt v3.4 – Remove Adapter Sequences from DNA Sequencing reads

cutadapt v3.4

:: DESCRIPTION

Cutadapt removes adapter sequences from DNA high-throughput sequencing data. This is usually necessary when the read length of the machine is longer than the molecule that is sequenced, such as in microRNA data.

::DEVELOPER

Marcel Martin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 cutadapt

:: MORE INFORMATION

Citation

Marcel Martin
Cutadapt removes adapter sequences from high-throughput sequencing reads
EMBnet.journal volume 17 pages 10–12

Cactus v2.0.1 – Genome Multiple Sequence Aligner

Cactus v2.0.1

:: DESCRIPTION

Cactus uses a cactus graph (aka cactus tree), a graph in which any edge is a member of at most one simple cycle, to construct a genome alignment. The aligner allows for arbitrary types of rearrangement and duplication, but favours alignments that create ‘chains’ of aligned bases.

::DEVELOPER

Benedict Paten (benedict (AT) soe.ucsc.edu)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • Python
  • C Compiler

:: DOWNLOAD

  Cactus

:: MORE INFORMATION

Citation

Cactus: Algorithms for genome multiple sequence alignment.
Paten B, Earl D, Nguyen N, Diekhans M, Zerbino D, Haussler D.
Genome Res. 2011 Sep;21(9):1512-28. doi: 10.1101/gr.123356.111. Epub 2011 Jun 10.

Velvet 1.2.10 – Sequence Assembler for Very Short Reads

Velvet 1.2.10

:: DESCRIPTION

Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454.Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs.

::DEVELOPER

Daniel Zerbino and Ewan Birney

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX

:: DOWNLOAD

 Velvet

:: MORE INFORMATION

Citation

D.R. Zerbino and E. Birney.
Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
Genome Research 18:821-829.

Oases 0.2.09 – De novo Transcriptome Assembler for very short reads

Oases 0.2.09

:: DESCRIPTION

Oases designed to heuristically assemble RNA-seq reads in the absence of a reference genome, across a broad spectrum of expression values and in presence of alternative isoforms. It achieves this by using an array of hash lengths, a dynamic filtering of noise, a robust resolution of alternative splicing events, and the efficient merging of multiple assemblies. It was tested on human and mouse RNA-seq data and is shown to improve significantly on the transABySS and Trinity de novo transcriptome assemblers.

::DEVELOPER

Daniel Zerbino

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Oases

:: MORE INFORMATION

Citation

Marcel H. Schulz, Daniel R. Zerbino, Martin Vingron and Ewan Birney
Oases: Robust de novo RNA-seq assembly across the dynamic range of expression levels
Bioinformatics (2012)doi: 10.1093/bioinformatics/bts094

SNPflow 1.3.5 – SNP Workflow Manager

SNPflow 1.3.5

:: DESCRIPTION

SNPflow is a freely available web application to automatically check the quality of SNP data employing the ABI 7900 HT-platform (e.g. TaqMan, KASPar Assays) or the Sequenom iPLEX platform: Single raw output files of plates are automatically merged and converted to genotype lists.

::DEVELOPER

GenEpi – Division of Genetic Epidemiology Innsbruck

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux
  • JRE

:: DOWNLOAD

 SNPflow

:: MORE INFORMATION

Citation

SNPflow: a lightweight application for the processing, storing and automatic quality checking of genotyping assays.
Weissensteiner H, Haun M, Schönherr S, Neuner M, Forer L, Specht G, Kloss-Brandstätter A, Kronenberg F, Coassin S.
PLoS One. 2013;8(3):e59508. doi: 10.1371/journal.pone.0059508.

HaploGrep 2.2.9 – Automatic mtDNA Haplogroup Classification

HaploGrep 2.2.9

:: DESCRIPTION

HaploGrep is a web application for finding the corresponding haplogroup to given mtDNA profiles based on Phylotree (mtDNA classification tree).

::DEVELOPER

GenEpi – Division of Genetic Epidemiology Innsbruck

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • JRE

:: DOWNLOAD

HaploGrep

:: MORE INFORMATION

Citation

HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing.
Weissensteiner H, Pacher D, Kloss-Brandstätter A, Forer L, Specht G, Bandelt HJ, Kronenberg F, Salas A, Schönherr S.
Nucleic Acids Res. 2016 Apr 15. pii: gkw233

MBRole 2.0 – Enrichment Analysis of Metabolomic data

MBRole 2.0

:: DESCRIPTION

MBRole (Metabolites Biological Role) is a server that performs functional enrichment analysis of a list of chemical compounds derived from a metabolomics experiment, which allows this list to be interpreted in biological terms.

::DEVELOPER

[Computational Systems Biology Group @CNB-CSIC]

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

MBROLE 2.0-functional enrichment of chemical compounds.
López-Ibáñez J, Pazos F, Chagoyen M.
Nucleic Acids Res. 2016 Apr 15. pii: gkw253.

Chagoyen, M. and Pazos, F. (2011)
MBRole: enrichment analysis of metabolomic data
Bioinformatics 27: 730-731