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http://www.bork.embl.de/software/smash/

A stand-alone metagenomic annotation and analysis pipeline suitable for data from Sanger and 454 sequencing technologies.

Proper citation: SmashCommunity (RRID:SCR_013245) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/books/NBK25500/

Entrez Programming Utilities are tools that provide access to Entrez data outside of the regular web query interface and may be helpful for retrieving search results for future use in another environment.
Additional information is available in the NCBI Bookshelf Short Courses Building Customized Data Pipelines Using the Entrez Programming Utilities (eUtils) and the NCBI PowerScripting course.
User Requirements: Please read for important information on scripting NCBI servers.
EInfo: Provides field index term counts, last update, and available links for each database.
ESearch: Searches and retrieves primary IDs (for use in EFetch, ELink, and ESummary) and term translations and optionally retains results for future use in the user''s environment.
EPost: Posts a file containing a list of primary IDs for future use in the user''s environment to use with subsequent search strategies.
ESummary: Retrieves document summaries from a list of primary IDs or from the user''s environment.
EFetch: Retrieves records in the requested format from a list of one or more primary IDs or from the user''s environment.
ELink: Checks for the existence of an external or Related Articles link from a list of one or more primary IDs. Retrieves primary IDs and relevancy scores for links to Entrez databases or Related Articles; creates a hyperlink to the primary LinkOut provider for a specific ID and database, or lists LinkOut URLs and Attributes for multiple IDs.
EGQuery: Provides Entrez database counts in XML for a single search using Global Query.
ESpell: Retrieves spelling suggestions.
SOAP Interface for Entrez Utilities
PMID to PMC ID Converter
Entrez DTDs
Demonstration Program
Announcement Mailing List
Leasing Data from the National Library of Medicine
Help Desk
User Requirements
Do not overload NCBI''s systems. Users intending to send numerous queries and/or retrieve large numbers of records from Entrez should comply with the following:
Run retrieval scripts on weekends or between 9 pm and 5 am Eastern Time weekdays for any series of more than 100 requests.
Send E-utilities requests to http://eutils.ncbi.nlm.nih.gov, not the standard NCBI Web address.
Make no more than 3 requests every 1 second.
Use the URL parameter email, and tool for distributed software, so that we can track your project and contact you if there is a problem.
NCBI''s Disclaimer and Copyright notice must be evident to users of your service. NLM does not claim the copyright on the abstracts in PubMed; however, journal publishers or authors may. NLM provides no legal advice concerning distribution of copyrighted materials, consult your legal counsel.

Proper citation: Entrez Utilities (RRID:SCR_013249) Copy   

•   Source: SciCrunch Registry

http://www.softpedia.com/get/Science-CAD/BrainVisa-Morphology-extensions.shtml

An extension projects providing computational tools for performing regional morphological measurements to assess groupwise differences and track morphological changes during maturation and aging. The extensions include computation of regional GM thickness, 3D gyrification index, sulcal lenght and depth and sulcal span. These tools are distributed in the form of plugins for a popular analysis package BrainVisa

Proper citation: BrainVisa Morphology extensions (RRID:SCR_013248) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/mirseq/files/

An R/Bioconductor based workflow for novel miRNA prediction from deep sequencing data.

Proper citation: miRSeqNovel (RRID:SCR_013257) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ligmap/files/

A tool for structural biology and drug design.

Proper citation: AutoMap (RRID:SCR_013095) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/dynamicprog/

A model-based statistical methods for base calling in Illumina''s next-generation sequencing platforms.

Proper citation: DynamicProg (RRID:SCR_013217) Copy   

•   Source: SciCrunch Registry

http://www.psy.ritsumei.ac.jp/~akitaoka/cataloge.html

Set of different illusions, including color illusions, motion illusions, and optic illusions. Most illusions are from Professor Akiyoshi Kitaoka of the Ritsumeikan University in Kyoto, Japan.

Proper citation: A Catalogue of Illusions (RRID:SCR_013186) Copy   

•   Source: SciCrunch Registry

http://www-rcf.usc.edu/~fsun/Programs/multiAlignFree/multiAlignFreemain.html

R package intended to implement a program for multiple alignment-free sequence comparison based on long genome sequence or NGS data.

Proper citation: muliAlignFree (RRID:SCR_013188) Copy   

•   Source: SciCrunch Registry

http://www.usphs.gov/

Commissioned Corps of the United States Public Health Service, is the federal uniformed service of the U.S. Public Health Service, and is one of the eight uniformed services of the United States.

Proper citation: U.S. Public Health Service Commissioned Corps (RRID:SCR_013104) Copy   

•   Source: SciCrunch Registry

http://www.cdc.gov/niosh/oep/funding.html

http://www.cdc.gov/niosh/oep/funding.html

Proper citation: National Institute for Occupational Safety and Health (RRID:SCR_013180) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages//2.10/bioc/html/CancerMutationAnalysis.html

Software package that implements gene and gene-set level analysis methods for somatic mutation studies of cancer.

Proper citation: CancerMutationAnalysis (RRID:SCR_013181) Copy   

•   Source: SciCrunch Registry

http://beads.sourceforge.net/

Software for a normalization scheme that corrects nucleotide composition bias, mappability variations and differential local DNA structural effects in deep sequencing data.

Proper citation: BEADS (RRID:SCR_013229) Copy   

•   Source: SciCrunch Registry

http://www.lifetechnologies.com/fr/fr/home/technical-resources/software-downloads/lifescope-genomic-analysis-software.html

Genomic Analysis Software designed to match the accuracy of the next generation 5500 Genetic Analyzers with Exact Call Chemistry (ECC).

Proper citation: LifeScope (RRID:SCR_013234) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/congrpe/

A de novo assembly algorithm for Next-Generation Sequencing technology.

Proper citation: CongrPE (RRID:SCR_013190) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/callsim/

A software application that provides evidence for the validity of base calls believed to be sequencing errors and it is applicable to Ion Torrent and 454 data.

Proper citation: CallSim (RRID:SCR_013192) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/sapas/

A RNA-seq method for polyA research.

Proper citation: SAPAS (RRID:SCR_013195) Copy   

•   Source: SciCrunch Registry

http://derisilab.ucsf.edu/index.php?software=105

An accurate and efficient algorithm for discovering canonical and non-canonical splice junctions in short read datasets.

Proper citation: HMMSplicer (RRID:SCR_013315) Copy   

•   Source: SciCrunch Registry

http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss

A software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data.

Proper citation: Trans-ABySS (RRID:SCR_013322) Copy   

•   Source: SciCrunch Registry

http://neuma.kobic.re.kr/

Software for estimating mRNA abundances from the whole transcriptome shotgun sequencing (RNA-Seq) data based on effective length normalization using uniquely mappable areas of gene and mRNA isoform models. Using the known transcriptome sequence model such as RefSeq, NEUMA pre-computes the numbers of all possible gene-wise and isoform-wise informative reads: the former being sequences mapped to all mRNA isoforms of a single gene exclusively and the latter uniquely mapped to a single mRNA isoform. The results are used to estimate the effective length of genes and transcripts, taking experimental distributions of fragment size into consideration. NEUMA covers a large proportion of genes and mRNA isoforms and offers a measure of consistency (''consistency coefficient'') for each gene between an independently measured gene-wise level and the sum of the isoform levels. NEUMA is applicable to both paired-end and single-end RNA-Seq data.

Proper citation: NEUMA (RRID:SCR_013324) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/chimerascan/

Software package that detects gene fusions in paired-end RNA sequencing (RNA-Seq) datasets. Used for detection of chimeric transcripts in high-throughput sequencing data.

Proper citation: chimerascan (RRID:SCR_013298) Copy   

•   Source: SciCrunch Registry