GenomeRunner 4.0 – Annotation and Enrichment of Next-Gen Sequencing Data

GenomeRunner 4.0

:: DESCRIPTION

GenomeRunner is a tool for automating genome exploration. It performs annotation and enrichment analyses of user-provided genomic regions (SNPs, ChIP-seq binding sites etc.) against >6,000 (human genome) epigenomic features available from the UCSC genome browser.

::DEVELOPER

GenomeRunner team

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

GenomeRunner

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Feb 1;28(3):419-20. doi: 10.1093/bioinformatics/btr666. Epub 2011 Dec 6.
GenomeRunner: automating genome exploration.
Dozmorov MG1, Cara LR, Giles CB, Wren JD.

Subread 2.0.2 / RSubread 2.6.1 – Processing Next-gen Sequencing data

Subread 2.0.2 / RSubread 2.6.1

:: DESCRIPTION

The Subread package is a toolkit for processing next-gen sequencing data

Subread: a very efficient and accurate read aligner suitable for mapping both gDNA-seq and RNA-seq reads (local alignments for RNA-seq reads). It can be used to map both short and long reads.
Subjunc: a specialized program developed for discovering exon-exon junctions and mapping RNA-seq reads (global alignments). It is highly accurate in discovering exon-exon junctions and mapping exon-spanning reads.
featureCounts: a program developed for summarizing reads to genomic features. It typically takes less than 4 minutes and uses at most 40MB of memory to summarize 20 million read pairs to 25k genes.

::DEVELOPER

WEHI Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX
R package & Bioconductor / C Compiler

:: DOWNLOAD

Subread / RSubread

:: MORE INFORMATION

Citation

Liao Y, Smyth GK and Shi W.
The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote.
Nucleic Acids Research, 41(10):e108, 2013

Liao Y, Smyth GK and Shi W.
featureCounts: an efficient general-purpose read summarization program.
arXiv:1305.3347, 2013

GenomeSmasher 1.0 – Creating Artificial Genomes for Next-gen Sequencing Simulations

GenomeSmasher 1.0

:: DESCRIPTION

GenomeSmasher is a set of tools used to create diploid FASTA files with containing snps, indels, duplications, deletions and translocations. These FASTA files can then be used in conjunction with next-generation sequencing simulators to artificially create sequencing experiments. The utility of these tools are to assess the performance and reliability of data analysis in next-generation sequencing pipelines.

::DEVELOPER

Bioinformatics Program, Division of Biomedical Statistics and Informatics, Mayo Clinic Research

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

GenomeSmasher

:: MORE INFORMATION

SNPSVM – A Support Vector Machine for Calling Variants from Next-gen Sequencing data

SNPSVM

:: DESCRIPTION

SNPSVM is a support vector machine based method for identifying sequence variants in next-gen sequencing data. It takes as input a BAM-formatted alignment of sequencing reads, and emits a VCF formatted file describing where all the SNPs (single nucleotide polymorphisms) are.

::DEVELOPER

Brendan O’Fallon , brendan.d.ofallon@aruplab.com

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Windows/MacOsX

:: DOWNLOAD

SNPSVM

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jun 1;29(11):1361-6. doi: 10.1093/bioinformatics/btt172. Epub 2013 Apr 24.
A support vector machine for identification of single-nucleotide polymorphisms from next-generation sequencing data.
O’Fallon BD, Wooderchak-Donahue W, Crockett DK.