the authors are trying to address? 2. What is the mo2va2on for addressing this problem? 3. What previous work has been done in this area? Are there pre-‐exis2ng tools that address this problem? 4. What computa2onal technologies did the authors make use of to create this tool?
authors make use of? 6. What is the input to this tool? 7. What is the output from this tool? 8. How did the authors test this tool? Was performance benchmarking included in their paper? 9. How did the authors evaluate whether this tool was giving biologically meaningful results?
enough memory to open the image, or the image may have been corrupted. Restart your computer, and then open the ﬁle again. If the red x still appears, you may have to delete the image and then insert it again.
gene composi2on of many samples in a single DNA sequencing reac2on. Pool samples and sequence Micah Hamady, et al., Nature Methods, 2008. Error-‐correc2ng barcodes for pyrosequencing hundreds of samples in mul2plex. Barcode the rRNA on a per-‐sample basis. >GCACCTGAGGACAGGCATGAGGAA… >GCACCTGAGGACAGGGGAGGAGGA… >TCACATGAACCTAGGCAGGACGAA… >CTACCGGAGGACAGGCATGAGGAT… >TCACATGAACCTAGGCAGGAGGAA… >GCACCTGAGGACACGCAGGACGAC… >CTACCGGAGGACAGGCAGGAGGAA… >CTACCGGAGGACACACAGGAGGAA… >GAACCTTCACATAGGCAGGAGGAT… >TCACATGAACCTAGGGGCAAGGAA… >GCACCTGAGGACAGGCAGGAGGAA…
wrapped in QIIME: uclust, BLAST, muscle, PyNAST, RDP classiﬁer, cdhit (full list in install documents). • Soeware can be installed na2vely on OS X and Linux, or via Virtual Machines. Pre-‐built Virtual Machines are available for all releases. • Parallel compu2ng supported across many environments (mul2-‐core/cluster/grid/cloud computers).
• Inves2gate the rela2ve temporal variability of body sites. • A small subset of the full data set to facilitate short run 2me: ~0.1% of the full sequence collec2on. • Sequenced on Illumina GAIIx; a subset of the samples also sequenced on 454. • The online tutorial contains details on all of the steps.
United States License. To view a copy of this license, visit hYp://crea2vecommons.org/licenses/by/3.0/us/ or send a leYer to Crea2ve Commons, 171 Second Street, Suite 300, San Francisco, California, 94105, USA. Feel free to use or modify these slides, but please credit me by placing the following aYribu2on informa2on where you feel that it makes sense: Greg Caporaso, www.caporaso.us.