Package: wnpp Severity: wishlist Owner: Steffen Moeller <steffen_moel...@gmx.de>
* Package name : qiime Version : 1.1.0 * URL : http://qiime.sf.net * License : GPL Description : Quantitative Insights Into Microbial Ecology QIIME (canonically pronounced ‘Chime’) is a pipeline for performing microbial community analysis that integrates many third party tools which have become standard in the field. A standard QIIME analysis begins with sequence data from one or more sequencing platforms, including Sanger, Roche/454, and Illumina GAIIx. With all the underlying tools installed, of which not all are yet available in Debian (or any other Linux distribution), QIIME can perform library de-multiplexing and quality filtering; denoising with PyroNoise; OTU and representative set picking with uclust, cdhit, mothur, BLAST, or other tools; taxonomy assignment with BLAST or the RDP classifier; sequence alignment with PyNAST, muscle, infernal, or other tools; phylogeny reconstruction with FastTree, raxml, clearcut, or other tools; alpha diversity and rarefaction, including visualization of results, using over 20 metrics including Phylogenetic Diversity, chao1, and observed species; beta diversity and rarefaction, including visualization of results, using over 25 metrics including weighted and unweighted UniFrac, Euclidean distance, and Bray-Curtis; summarization and visualization of taxonomic composition of samples using pie charts and histograms; and many other features. . QIIME includes parallelization capabilities for many of the computationally intensive steps. By default, these are configured to utilize a mutli-core environment, and are easily configured to run in a cluster environment. QIIME is built in Python using the open-source PyCogent toolkit. It makes extensive use of unit tests, and is highly modular to facilitate custom analyses. -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20100626231912.23778.53611.report...@toshiba.siemens
