Author: tille Date: Mon Jun 28 06:58:53 2010 New Revision: 2237 URL: http://svn.debian.org/viewsvn/blends?rev=2237&view=rev
Log: Added qiime as propective package Modified: projects/med/trunk/debian-med/tasks/bio Modified: projects/med/trunk/debian-med/tasks/bio URL: http://svn.debian.org/viewsvn/blends/projects/med/trunk/debian-med/tasks/bio?rev=2237&view=diff&r1=2237&r2=2236&p1=projects/med/trunk/debian-med/tasks/bio&p2=projects/med/trunk/debian-med/tasks/bio ============================================================================== --- projects/med/trunk/debian-med/tasks/bio (original) +++ projects/med/trunk/debian-med/tasks/bio Mon Jun 28 06:58:53 2010 @@ -3213,6 +3213,40 @@ SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. +Depends: qiime +WNPP: 587275 +Homepage: http://qiime.sf.net +License: GPL +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/qiime/trunk/?rev=0&sc=0 +Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/qiime/trunk/ +Responsible: Steffen Moeller <[email protected]> +Pkg-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. + Comment: Several related R packages are listed at CRAN: http://cran.r-project.org/web/views/Genetics.html _______________________________________________ Blends-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/blends-commit
