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- interested in using the MetaSim software package? A description of MetaSim is below. One note: It appears to be a capable simulator, but MetaSim is closed source...9 KB (1,269 words) - 15:21, 17 August 2017
- taxonomic profile for the sequences (uniform, for now) to be used by MetaSim. Run MetaSim simulation on the chosen sequences to generate some number, say 100...3 KB (411 words) - 15:24, 17 August 2017
- (e.g. masked vs. not) SQL db UCD accounts (bobcat, genbeo) Simulations MetaSim pretty easy to use might have to do some scripting to generate input files...1 KB (161 words) - 14:47, 17 August 2017
- or other conversation system how to have huge discussions? Let's try it. MetaSim problems with command line how many species to include and how related (random...1 KB (202 words) - 14:50, 17 August 2017
- Simulations Martin's data is on bobcat.genomecenter.ucdavis.edu/AMPHORA website metaSim, JGI simulation paper (datasets available, not clear exactly how done) Make...2 KB (278 words) - 14:46, 17 August 2017
- for each simulation, choose N sequences to be fragmented into reads (by MetaSim). How many sequences do we choose for fragmentation, i.e., what should N...11 KB (1,869 words) - 14:26, 22 August 2017
- data set) Sam: simulations fixed bug with Martin AMPHORA only maps some metaSim reads to profile Is it OK to have a random number of reads/taxa per run...2 KB (363 words) - 14:56, 17 August 2017
- from AMPHORA reference sequence data base. Breaking up into reads using metasim. using amphora to use trimmed alignment using AMPHORA hhm. Calling marker...3 KB (490 words) - 14:55, 17 August 2017
- Erickson C, Giertych B, Akhter H, Wang L, Stewart A, Parenti J, Wang B, Wen S, Sim S, Quenneville E, Hansen K, Frisch S, Hu G (2022) Matrix from urine stem cells...22 KB (3,690 words) - 11:04, 30 April 2024
- coming out - should I fully mask all of the states that are coming out? Metasim has a bunch of problems....4 KB (645 words) - 14:53, 17 August 2017
- commercially available meta-substituted boronic acid/esters from Boron Molecular as shown here. 3. We already ordered several other meta-substituted boronic...20 KB (2,380 words) - 23:11, 28 June 2018
- varied Using AMPHORA as a backbone to some components of the simulations METASIM used as part of the simulation POssibly may be doing some weird things w/...6 KB (762 words) - 13:55, 22 August 2017
- directory: sims-RefDBs-rpoB-n20-m5/sims-rpoB-n500m18r2000q-1p400u20/ sim1 subdirectory: sim1-rpoB-n500m18r2000q-1p400u20/ alignment files in the sim1 subdirectory:...9 KB (1,514 words) - 15:20, 17 August 2017
- dir="ltr"> <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> <meta name="generator" content="MediaWiki 1.13.2" /> <meta name="keywords"...27 KB (4,040 words) - 02:30, 16 June 2015
- Jenna Morgan about in vitro simulations of metagenomic sequencing. Media:MetaSim long.pdf Discussion of simulators and simulated data sets that are already...7 KB (866 words) - 13:53, 22 August 2017
- predicted by EcoSim. In most cases, a cutoff between 98% and 99% best approximated ecotypes, but in some genera the clusters generated by EcoSim were closest...30 KB (3,894 words) - 14:41, 22 August 2017
- Rockett, R. J., Arnott, A., Lam, C., Sadsad, R., Timms, V., Gray, K. A., ... & Sim, E. M. (2020). Revealing COVID-19 transmission in Australia by SARS-CoV-2...20 KB (3,291 words) - 00:55, 12 November 2020
- full-length sequences for a given gene family from the AMPHORA database, uses the MetaSim program to fragment these sequences into simulated metagenomic reads, translates...28 KB (3,880 words) - 14:17, 22 August 2017
- data is currently impractical for complex communities. Along with MetaSim, the MetaPASSAGE workflow incorporates several well-known programs, including...113 KB (14,604 words) - 14:43, 22 August 2017
- developing a simulation pipeline, which will most likely be based on the MetaSim program described in a paper by Richter et al [1]. Steve Kembel and Samantha...61 KB (8,556 words) - 14:14, 22 August 2017
