gage.cbcb.umd.edu

GAGE

GAGE is an evaluation of the very latest large-scale genome assembly algorithms. We have organized this "bake-off" as an attempt to produce a realistic assessment of genome assembly software in a rapidly changing field of next-generation sequencing. The main results of GAGE have now been published in the journal. GAGE: A critical evaluation of genome assemblies and assembly algorithms. Why do we need GAGE? How much sequencing coverage do I need for my genome project? Here are some differences:. We will c...

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GAGE | gage.cbcb.umd.edu Reviews

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GAGE is an evaluation of the very latest large-scale genome assembly algorithms. We have organized this bake-off as an attempt to produce a realistic assessment of genome assembly software in a rapidly changing field of next-generation sequencing. The main results of GAGE have now been published in the journal. GAGE: A critical evaluation of genome assemblies and assembly algorithms. Why do we need GAGE? How much sequencing coverage do I need for my genome project? Here are some differences:. We will c...

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1 main page

2 genome assemblers

3 data sets

4 recipes

5 results

6 twitter

7 what is gage

8 genome research

9 all natural ingredients

10 completely open protocols

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GAGE | gage.cbcb.umd.edu Reviews

https://gage.cbcb.umd.edu

GAGE is an evaluation of the very latest large-scale genome assembly algorithms. We have organized this "bake-off" as an attempt to produce a realistic assessment of genome assembly software in a rapidly changing field of next-generation sequencing. The main results of GAGE have now been published in the journal. GAGE: A critical evaluation of genome assemblies and assembly algorithms. Why do we need GAGE? How much sequencing coverage do I need for my genome project? Here are some differences:. We will c...

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gage.cbcb.umd.edu

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Genome assemblers under evaluation in GAGE

http://gage.cbcb.umd.edu//assemblers/index.html

What genome assemblers are under evaluation? We are evaluating the performance of the following genome assemblers on our data sets:. ABySS (Assembly By Short Sequencing) (Birol et al). A denovo assembler for short read sequence data which uses a distributed representation of a de Bruijn graph, allowing parallel computation of the assembly algorithm across a network of commodity computers. Developed at Canada's Michael Smith Genome Sciences Centre. ALLPATHS-LG (Gnerre et al). A de Bruijn graph-based.

2

GAGE

http://gage.cbcb.umd.edu//index.html

GAGE is an evaluation of the very latest large-scale genome assembly algorithms. We have organized this "bake-off" as an attempt to produce a realistic assessment of genome assembly software in a rapidly changing field of next-generation sequencing. The main results of GAGE have now been published in the journal. GAGE: A critical evaluation of genome assemblies and assembly algorithms. Why do we need GAGE? How much sequencing coverage do I need for my genome project? Here are some differences:. We will c...

3

GAGE assembly results

http://gage.cbcb.umd.edu//results/index.html

Final assemblies now available:. Download all assemblies for this genome. Download all assemblies for this genome. H sapies Chr 14. Download all assemblies for this genome. Download all assemblies for this genome. Download the analysis scripts. Download MUMmer 3.23, available here. Run: tar xvzf MUMmer3.23.tar.gz. Run: cd MUMmer3.23. Run: tar xvzf gage-validation.tar.gz. Run: sh getCorrectnessStats.sh <Reference Fasta> <Contig Fasta> <Scaffold Fasta>. Download an updated version of the analysis scripts.

4

GAGE recipes

http://gage.cbcb.umd.edu//recipes/index.html

What recipes were used for each genome assembly? Links to recipes for each genome assembler, which include instructions and all necessary scripts to reproduce the results:.

5

Genome assemblers under evaluation in GAGE

http://gage.cbcb.umd.edu/assemblers/index.html

What genome assemblers are under evaluation? We are evaluating the performance of the following genome assemblers on our data sets:. ABySS (Assembly By Short Sequencing) (Birol et al). A denovo assembler for short read sequence data which uses a distributed representation of a de Bruijn graph, allowing parallel computation of the assembly algorithm across a network of commodity computers. Developed at Canada's Michael Smith Genome Sciences Centre. ALLPATHS-LG (Gnerre et al). A de Bruijn graph-based.

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ccb.jhu.edu

CCB Software

http://ccb.jhu.edu/software.shtml

Next-Generation Sequence Alignment Software. Genome Assembly and Large-Scale Genome alignment. Next-generation sequence alignment software. TopHat-Fusion is an enhanced version of TopHat with the ability to align reads across fusion points, which results from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome. HISAT is a new, highly efficient system for aligning RNA-seq reads. HISAT uses a new indexing scheme, hierarchical indexing, which is inherentl...

ccb.jhu.edu

Downloads

http://ccb.jhu.edu/downloads.shtml

Are evaluations of contiguity and accuracy of assemblies that are generated by some of most commonly used genome assemblers. GAGE-B (for assemblies of bacterial organisms) follows the standards set by GAGE. This page contains links to many of the genomes we have assembled. The "Data download" link will take you to a page where you can get the assembly of the genome itself, along with genome annotation (in some cases). See our paper in Genome Biology. On the cow assembly. Baylor College of Medicine.

gene.neuralcortex.com

neuralcortex

http://www.gene.neuralcortex.com/a_assembly.htm

Ultra Fast De Novo Assembly using Storm. A demonstration de novo assembler based on Storm technology assembled human chromosome 14 in just 10 seconds, roughly a hundred. Times faster that current assemblers running on expensive computers. Standard assembly test suite, for which there are good comparative results. The assembly used a 40x coverage for HC-14's 91 million base pair sequence. The complete assembly process from raw data to assembled contigs runs on gpu hardware. Three gpus were run in parallel.

gene.neuralcortex.com

Ultra Fast Technology for Genetic Computation

http://www.gene.neuralcortex.com/index.htm

A set of novel. Computational methods used to develop. Ultra fast solutions for genetics and bio- computational problems such as. DNA assembly, alignment, and classification. Its power is rooted in a highly parallel multidimensional indexing system called. High level architecture of the. Gene Storm further enhances performance by. The full functionality and. Power of next generation GPU architectures. Can align an entire human genome at 20x coverage. S, 100 - 1000 times faster than comparable tools.

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gage.cbcb.umd.edu

GAGE

GAGE is an evaluation of the very latest large-scale genome assembly algorithms. We have organized this "bake-off" as an attempt to produce a realistic assessment of genome assembly software in a rapidly changing field of next-generation sequencing. The main results of GAGE have now been published in the journal. GAGE: A critical evaluation of genome assemblies and assembly algorithms. Why do we need GAGE? How much sequencing coverage do I need for my genome project? Here are some differences:. We will c...

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GAGE is a three piece rock outfit that was formed in 2007 comprising of Jason Horseman on lead vocals and drums; Llewellyn Burger on guitar and backing vocals and Johan Wooberg aka Johnny Woo on bass guitar and backing vocals. To date GAGE has recorded three albums, the first released in 2010 titled Empty Spaces , the second in 2014 titled Break the Silence and the third in 2017 titled For the Fans . GAGE released their first music video on YouTube titled All that I am taken from their second album Break...