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http://www.baseclear.com/landingpages/basetools-a-wide-range-of-bioinformatics-solutions/sspacev12/

A stand-alone software program for scaffolding pre-assembled contigs using paired-read data. Main features are: a short runtime, multiple library input of paired-end and/or mate pair datasets and possible contig extension with unmapped sequence reads.

Proper citation: SSPACE (RRID:SCR_005056) Copy   

•   Source: SciCrunch Registry

http://meringlab.org/software/hpc-clust/

A set of tools designed to cluster large numbers (>1 million) of pre-aligned nucleotide sequences. It performs the clustering of sequences using the Hierarchical Clustering Algorithm (HCA). There are currently three different cluster metrics implemented: single-linkage, complete-linkage, and average-linkage. In addition, there are currently four sequence distance functions implemented, these are: identity (gap-gap counting as match), nogap (gap-gap being ignored), nogap-single (like nogap, but consecutive gap-nogap''s count as a single mismatch), tamura (distance is calculated with the knowledge that transitions are more likely than transversions). One advantage that HCA has over other algorithms is that instead of producing only the clustering at a given threshold, it produces the set of merges occuring at each threshold. With this approach, the clusters can afterwards very quickly be reported for every arbitrary threshold with little extra computation. This approach also allows the plotting of the variation of number of clusters with clustering threshold without requiring the clustering to be run for each threshold independently. Another feature of the way HPC-CLUST is implemented is that the single-, complete-, and average-linkage clusterings can be computed in a single run with little overhead.

Proper citation: HPC-CLUST (RRID:SCR_005052) Copy   

•   Source: SciCrunch Registry

http://plaza.ufl.edu/xywang/Mpick.htm

A modularity-based clustering software for Operational Taxonomic Unit (OTU) picking of 16S rRNA sequences. The algorithm does not require a predetermined cut-off level, and our simulation studies suggest that it is superior to existing methods that require specified distance or variance levels to define OTUs.

Proper citation: M-pick (RRID:SCR_004995) Copy   

•   Source: SciCrunch Registry

http://www.manchester.ac.uk/

Public research university in Manchester, England, formed in 2004 by merger of University of Manchester Institute of Science and Technology and Victoria University of Manchester. Second largest university in United Kingdom by enrollment.

Proper citation: University of Manchester; Manchester; United Kingdom (RRID:SCR_004996) Copy   

•   Source: SciCrunch Registry

https://bxcell.com/

Commercial supplier and developer of in vivo antibodies. Provides antibodies and antibody production services.

Proper citation: Bio X Cell (RRID:SCR_004997) Copy   

•   Source: SciCrunch Registry

http://plaza.ufl.edu/sunyijun/ES-Tree.htm

Software for hierarchical Clustering Analysis of Millions of 16S rRNA Pyrosequences in Quasi-linear Time.

Proper citation: ESPRIT-Tree (RRID:SCR_005045) Copy   

•   Source: SciCrunch Registry

http://english.hust.edu.cn/

Public research university located in Guanshan Subdistrict, Hongshan District, Wuhan, Hubei province, China.

Proper citation: Huazhong University of Science and Technology; Wuhan; China (RRID:SCR_005047) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/MBCluster.Seq/index.html

Software to cluster genes based on Poisson or Negative-Binomial model for RNA-Seq or other digital gene expression (DGE) data.

Proper citation: MBCluster.Seq (RRID:SCR_005079) Copy   

•   Source: SciCrunch Registry

http://www.ku.edu/

Public research university with its main campus in Lawrence, Kansas, and several satellite campuses, research and educational centers, medical centers, and classes across the state of Kansas.

Proper citation: University of Kansas; Kansas; USA (RRID:SCR_005075) Copy   

•   Source: SciCrunch Registry

http://www.biomedcentral.com/1471-2105/13/189

An algorithm to use optical map information directly within the de Bruijn graph framework to help produce an accurate assembly of a genome that is consistent with the optical map information provided. AGORA takes as input two data structures: OpMap ? an ordered list of fragment sizes representing the optical map; and Edges ? a list of de Bruijn graph edges with their corresponding sequences.

Proper citation: AGORA (RRID:SCR_005070) Copy   

•   Source: SciCrunch Registry

https://github.com/AlexeyG/GRASS

A generic algorithm for scaffolding next-generation sequencing assemblies.

Proper citation: GRASS (RRID:SCR_005071) Copy   

•   Source: SciCrunch Registry

http://www.bioinf.boku.ac.at/pub/MapAl/

A software tool for RNA-Seq expression profiling that builds on the established programs Bowtie and Cufflinks. Allowing an incorporation of ''gene models'' already at the alignment stage almost doubles the number of transcripts that can be measured reliably.

Proper citation: MapAl (RRID:SCR_004938) Copy   

•   Source: SciCrunch Registry

http://www.open.ac.uk/

Public research university and the largest university in the UK for undergraduate education. The majority of the OU's undergraduate students are based in the United Kingdom and principally study off-campus; many of its courses can also be studied anywhere in the world.

Proper citation: Open University; Milton Keynes; United Kingdom (RRID:SCR_004931) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/apps/mediawiki/amos/index.php?title=Bambus2

Software for scaffolding to address some of the challenges encountered when analyzing metagenomes. Scaffolding represents the task of ordering and orienting contigs by incorporating additional information about their relative placement along the genome. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with great flexibility in choosing the scaffolding parameters. In particular, Bambus is able to accept contig linking data other than specified by mate-pairs. Such sources of information include alignment to a reference genome (Bambus can directly use the output of MUMmer), physical mapping data, or information about gene synteny.

Proper citation: Bambus (RRID:SCR_005068) Copy   

•   Source: SciCrunch Registry

http://www.medicine.uiowa.edu/

Medical school of the University of Iowa, located in Iowa City, in the U.S. state of Iowa.

Proper citation: University of Iowa Carver College of Medicine; Iowa; USA (RRID:SCR_005064) Copy   

•   Source: SciCrunch Registry

http://www.comp.hkbu.edu.hk/~chxw/software/G-BLASTN.html

A GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST. It can produce exactly the same results as NCBI-BLAST, and it also has very similar user commands. It also supports a pipeline mode, which can fully utilize the GPU and CPU resources when handling a batch of medium to large sized queries.

Proper citation: G-BLASTN (RRID:SCR_005062) Copy   

•   Source: SciCrunch Registry

http://sri.com/

Independent, nonprofit research institute conducting client sponsored research and development for government agencies, commercial businesses, foundations, and other organizations. SRI also brings its innovations to the marketplace by licensing its intellectual property and creating new ventures. SRI was founded as Stanford Research Institute in 1946 by a group of West Coast industrialists and Stanford University. SRI formally separated from the University in 1970, and we changed our name to SRI International in 1977.

Proper citation: Stanford Research Institute International (RRID:SCR_004926) Copy   

•   Source: SciCrunch Registry

http://www.carleton.ca/

Public comprehensive university in Ottawa, Ontario, Canada. Founded in 1942 as Carleton College, a private, non-denominational evening college to serve returning World War II.

Proper citation: Carleton University; Ontario; Canada (RRID:SCR_011136) Copy   

•   Source: SciCrunch Registry

https://www.aldevron.com/

Contract manufacturing services company, specializing in plasmid DNA manufacturing, protein services and antibody development.Producesg high quality plasmid DNA, proteins, enzymes, antibodies, and other biologicals in support of clients objectives.

Proper citation: Aldevron (RRID:SCR_011017) Copy   

•   Source: SciCrunch Registry

http://www.mrc.ac.uk/Fundingopportunities/index.htm

The Medical Research Council is a publicly-funded organization dedicated to improving human health. We support research across the entire spectrum of medical sciences, in universities and hospitals, in our own units, centers and institutes in the UK, and in our units in Africa.

Proper citation: Medical Research Council (RRID:SCR_011018) Copy   

•   Source: SciCrunch Registry