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http://www.ebi.ac.uk/gxa/

Gene Expression Atlas is a semantically enriched database of meta-analysis based summary statistics over a curated subset of ArrayExpress Archive, servicing queries for condition-specific gene expression patterns as well as broader exploratory searches for biologically interesting genes/samples. The EBI Gene Expression Atlas Blog discusses ideas, features and problems of creating a large scale meta-analytical atlas of gene expression from publicly available microarray data. Atlas REST API provides all the results available in the main web application in a pragmatic, easy to use form - simple HTTP GET queries as input and either JSON or XML formats as output. Gene Expression Atlas goals: 1. Provision of a statistically robust framework for integration of gene expression experiment results across different platforms at a meta-analytical level 2. A simple interface for identifying strong differential expression candidate genes in conditions of interest 3. Integration of ontologies for high quality annotation of gene and sample attributes 4. Construction of new gene expression summarized views, with a view to analysis of putative signaling pathway targets, discovery of correlated gene expression patterns and the identification of condition/tissue-specific patterns of gene expression.

Proper citation: Gene Expression Atlas (RRID:SCR_007989) Copy   

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http://www.ensembl.org/info/docs/tools/vep/index.html

Data analysis service to predict the functional consequences of known and unknown variants.

Proper citation: Variant Effect Predictor (RRID:SCR_007931) Copy   

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http://etest.vbi.vt.edu/etblast3/

eTBLAST is a unique search engine for searching biomedical literature. Our service is very different from PubMed. While PubMed searches for keywords, our search engine lets you input an entire paragraph and returns MEDLINE abstracts that are similar to it. This is something like PubMed''s Related Articles feature, only better because it runs on your unique set of interests. For example, input the abstract of an unpublished paper or a grant proposal into our engine, and with the touch of a button you''ll be able to find every abstract in MEDLINE dealing with your topic. No more guessing whether your set of keywords has found all the right papers. No more sorting through hundreds of papers you don''t care about to find the handful you were looking for--our search engine does it for you. When most people use PubMed to search MEDLINE they pick one or two keywords to describe their topic, then browse through a long list of results. When they find a paper that looks interesting they click on its Related Articles, in hopes of finding more papers like that one. If they find another relevant paper, they explore it''s related articles--and so on. This process of culling long lists of documents by hand makes literature searching tedious and time consuming. We make it easier for you by providing better results the first time, and then allowing you to automatically combine the papers you care about for a second round. Our Iterate feature allows you to checkmark the abstracts you found interesting in the first round and combine them all to create a new query. It''s like rolling several Related Articles lists into one. * We sort our results by relevance, while PubMed sorts by date. * We save you the time and effort of creating a complicated query. * We let you iterate your search over several good papers to narrow your focus. * We provide you the full MEDLINE abstract in our results, and a link to the PubMed page. * We can send your results straight to your email so you never lose a reference or forget where you found it. * This absolutely free service is provided by the University of Texas Southwestern Medical Center. No registration necessary!

Proper citation: eTBlast (RRID:SCR_008188) Copy   

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http://minia.genouest.org/

A short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day.

Proper citation: Minia (RRID:SCR_004986) Copy   

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http://smart.embl.de/

Software tool for identification and annotation of genetically mobile domains and analysis of domain architectures.

Proper citation: SMART (RRID:SCR_005026) Copy   

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http://www.cs.helsinki.fi/u/lmsalmel/mip-scaffolder/

A software program for scaffolding contigs produced by fragment assemblers using mate pair data such as those generated by ABI SOLiD or Illumina Genome Analyzer.

Proper citation: MIP Scaffolder (RRID:SCR_005072) Copy   

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http://petrov.stanford.edu/cgi-bin/Tlex.html

Software package for fast and accurate discovery, annotation, re-annotation and population analysis of Transposable Elements using Next-Generation Sequencing data.

Proper citation: T-lex (RRID:SCR_005134) Copy   

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http://woldlab.caltech.edu/rnaseq

Software for Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq. Its functions are to (i) assign reads that map uniquely in the genome to their site of origin and, for reads that match equally well to several sites (''multireads''), assign them to their most likely site(s) of origin; (ii) detect splice-crossing reads and assign them to their gene of origin; (iii) organize reads that cluster together, but do not map to an already known exon, into candidate exons or parts of exons; and (iv) calculate the prevalence of transcripts from each known or newly proposed RNA, based on normalized counts of unique reads, spliced reads and multireads. The new candidate RNA regions produced can be thought of as ESTs, and, like ESTs, some are provisionally appended to existing gene models if they meet several additional criteria. Remaining unassigned candidate transcribed regions (labeled RNAFAR features) can then be used in conjunction with other confirming data to develop new or revised gene models.

Proper citation: ERANGE (RRID:SCR_005240) Copy   

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http://www.broadinstitute.org/cancer/cga/rna-seqc

Java software which computes a series of quality control metrics for RNA-seq data and can compare sequencing quality across different samples or experiments to evaluate different experimental parameters. The input can be one or more BAM files, and the output consists of HTML reports and tab delimited files of metrics data.

Proper citation: RNA-SeQC (RRID:SCR_005120) Copy   

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http://cbrc.kaust.edu.sa/readscan/

A highly scalable parallel software program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets.

Proper citation: READSCAN (RRID:SCR_005204) Copy   

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http://odin.mdacc.tmc.edu/~xsu1/VirusSeq.html

An algorithmic software tool for detecting known viruses and their integration sites using next-generation sequencing of human cancer tissue. VirusSeq takes FASTQ files (paired-end reads) as input.

Proper citation: VirusSeq (RRID:SCR_005206) Copy   

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http://smithlab.usc.edu/methpipe/

A computational pipeline for analyzing bisulfite sequencing data.

Proper citation: MethPipe (RRID:SCR_005168) Copy   

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http://snpeff.sourceforge.net/

Genetic variant annotation and effect prediction software toolbox that annotates and predicts effects of variants on genes (such as amino acid changes). By using standards, such as VCF, SnpEff makes it easy to integrate with other programs.

Proper citation: SnpEff (RRID:SCR_005191) Copy   

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https://code.google.com/p/simrare/

A stand-alone executable software with user-friendly graphical interface implemented in Python/C++ for rare variant association studies. It is designed as a unified simulation framework to provide an unbiased and easy manner to evaluate association methods, including novel methods, under a broad range of choice of biological contexts. It consists of three modules, variant data simulator, genotype/phenotype generator and association method evaluator. SimRare generates variant data for gene regions using forward-time simulation which incorporates realistic population demographic and evolutionary scenarios. For phenotype data it is capable of generating both case-control and quantitative traits. The phenotypic effects of variants can be detrimental, protective or non-causal. SimRare has a graphical user interface which allows for easy entry of genetic and phenotypic parameters. Simulated data can be written into external files in a standard format. For novel association method implemented in R it can be imported into SimRare, which has been equipped built in functions to evaluate performance of new method and visually compare it with currently available ones in an unbiased manner.

Proper citation: SimRare (RRID:SCR_005226) Copy   

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http://phast.wishartlab.com/

A web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids. It accepts either raw DNA sequence data or partially annotated GenBank formatted data and rapidly performs a number of database comparisons as well as phage cornerstone feature identification steps to locate, annotate and display prophage sequences and prophage features. Relative to other prophage identification tools, PHAST is up to 40 times faster and up to 15% more sensitive. It is also able to process and annotate both raw DNA sequence data and Genbank files, provide richly annotated tables on prophage features and prophage quality and distinguish between intact and incomplete prophage. PHAST also generates downloadable, high quality, interactive graphics that display all identified prophage components in both circular and linear genomic views. Databases available for download include Virus DB, Prophage and virus DB, Bacteria DB, and PHAST result DB. Pre-calculated genomes for viewing are also available.

Proper citation: PHAge Search Tool (RRID:SCR_005184) Copy   

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https://github.com/ruping/Breakpointer

A fast tool for locating sequence breakpoints from the alignment of single end reads (SE) produced by next generation sequencing (NGS). It adopts a heuristic method in searching for local mapping signatures created by insertion/deletions (indels) or more complex structural variants(SVs). With current NGS single-end sequencing data, the output regions by Breakpoint mainly contain the approximate breakpoints of indels and a limited number of large SVs. Notably, Breakpointer can uncover breakpoints of insertions which are longer than the read length. Breakpointer also can find breakpoints of many variants located in repetitive regions. The regions can be used not only as a extra support for SV predictions by other tools (such as by split-read method), but also can serve as a database for searching variants which might be missed by other tools. Breakpointer is a command line tool that runs under linux system. Breakpointer takes advanage of two local mapping features of single-end reads as a consequence of indel/SVs: 1) non-uniform read distribution (depth skewness) and 2) misalignments at the boundaries of indel/SVs. These features are summarized as breakpoint signature. Breakpointer proceeds in three stages in capturing this signature. It is implemented in C++ and perl. Input is the file or files containing alignments of single-end reads against a reference genome (in .BAM format). Output is the predicted regions containing potential breakpoints of SVs (in .GFF format). To be able to read in .BAM files, Breakpointer requires bamtools API, which users should install beforehand.

Proper citation: Breakpointer (RRID:SCR_005254) Copy   

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http://www.genoscope.cns.fr/externe/gmorse/

Software aimed at using RNA-Seq short reads to build de novo gene models. First, candidate exons are built directly from the positions of the reads mapped on the genome (without any ab initio assembly of the reads), and all the possible splice junctions between those exons are tested against unmapped reads : the testing of junctions is directed by the information available in the RNA-Seq dataset rather than a priori knowledge about the genome. Exons can thus be chained into stranded gene models.

Proper citation: G-Mo.R-Se (RRID:SCR_005273) Copy   

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http://ingap.sourceforge.net/

Software mining pipeline guided by a Bayesian principle to detect single nucleotide polymorphisms, insertion and deletions by comparing high-throughput pyrosequencing reads with a reference genome of related organisms. This pipeline is extended to identify and visualize large-size structural variations, including insertions, deletions, inversions and translocations.

Proper citation: inGAP (RRID:SCR_005261) Copy   

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http://sv.gersteinlab.org/pemer/

Software package as computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. Package is composed of three modules, PEMer workflow, SV-Simulation and BreakDB. PEMer workflow is a sensitive software for detecting SVs from paired-end sequence reads. SV-Simulation randomly introduces SVs into a given genome and generates simulated paired-end reads from novel genome.

Proper citation: PEMer (RRID:SCR_005263) Copy   

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https://code.google.com/p/phantompeakqualtools/

Software package that computes quick but highly informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.

Proper citation: phantompeakqualtools (RRID:SCR_005331) Copy   

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