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http://ab.inf.uni-tuebingen.de/software/megan/
Software for analyzing metagenomes.
Proper citation: MEGAN (RRID:SCR_011942) Copy
http://vm-lux.embl.de/~kultima/MOCAT//
Software package for analyzing metagenomics datasets.
Proper citation: MOCAT (RRID:SCR_011943) Copy
A clustering algorithm focusing on noise injection for subsequent cluster validation.
Proper citation: pyGCluster (RRID:SCR_011944) Copy
http://artiva.gene-networks.net/artiva-2/
Algorithm available in a R package that is a statistical framework to infer time-varying structures of gene-regulation networks.
Proper citation: ARTIVA (RRID:SCR_011946) Copy
http://www.phrap.org/phredphrapconsed.html
A software program for assembling shotgun DNA sequence data.
Proper citation: Phrap (RRID:SCR_011917) Copy
http://denovoassembler.sourceforge.net/
Software for a massively distributed metagenome assembler that is coupled with Ray Communities, which profiles microbiomes based on uniquely-colored k-mers.
Proper citation: Ray Meta (RRID:SCR_011918) Copy
http://genome.ucsc.edu/cgi-bin/hgBlat?command=start
Software designed to quickly find sequences of 95% and greater similarity of length 25 bases or more.
Proper citation: BLAT (RRID:SCR_011919) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2019. Delivers public cloud infrastructure that''s business grade, open source-based, and developer focused., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: HP Public Cloud (RRID:SCR_011873) Copy
High-performance cloud infrastructure and big data analytics company, offering organizations of any size the best public and hybrid cloud infrastructure for today''s demanding real-time web and mobile applications.
Proper citation: Joyent (RRID:SCR_011874) Copy
http://www.bios.unc.edu/research/genomic_software/BBSeq/
A Powerful and Flexible Approach to the Analysis of RNA Sequence Count Data.
Proper citation: BBSeq (RRID:SCR_011877) Copy
http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/
Software for an iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth.
Proper citation: IDBA-UD (RRID:SCR_011912) Copy
http://i.cs.hku.hk/~alse/hkubrg/projects/metaidba/
Software for an iterative De Bruijn Graph De Novo short read assembler specially designed for de novo metagenomic assembly. (Please note that MetaIDBA is out of maintainance now, we recommend using IDBA-UD instead which generally performs better.)
Proper citation: Meta-IDBA (RRID:SCR_011913) Copy
http://www.windowsazure.com/en-us/
An open and flexible cloud platform that enables you to quickly build, deploy and manage applications across a global network of Microsoft-managed datacenters.
Proper citation: Windows Azure (RRID:SCR_011880) Copy
https://basespace.illumina.com/home/sequence
Cloud platform to be directly integrated in to the industry?s leading sequencing platforms, with no cumbersome and time consuming data transfer steps.
Proper citation: BaseSpace (RRID:SCR_011881) Copy
https://sites.google.com/site/biovlab/
Cloud Computing and a graphical workflow composer that uses distributed computing resources on demand.''''
Proper citation: BioVLAB (RRID:SCR_011882) Copy
Offers genome analysis resources for cloud computing platforms such as Amazon EC2.
Proper citation: CloudBioLinux (RRID:SCR_011883) Copy
http://weizhong-lab.ucsd.edu/rammcap/cgi-bin/rammcap.cgi
Metagenomic software pipeline for analysis and comparison of very large metagenomes with fast clustering and functional annotation.
Proper citation: RAMMCAP (RRID:SCR_011927) Copy
http://euler.bc.edu/marthlab/scotty/scotty.php/
A tool to assist in the designing of RNA Seq experiments that have adequate power to detect differential expression at the level required to achieve experimental aims.
Proper citation: Scotty (RRID:SCR_011889) Copy
http://www.cs.ucr.edu/~jianxing/IsoInfer.html
A C/C++ program to infer isoforms based on short RNA-Seq (single-end and paired-end) reads, exon-intron boundary and TSS/PAS information.
Proper citation: IsoInfer (RRID:SCR_011892) Copy
http://bioinformatics.childhealthresearch.org.au/software/fusionfinder/
A perl-based software package, which can be used to find fusion transcript candidates in RNA-Seq data.
Proper citation: FusionFinder (RRID:SCR_011894) Copy
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