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Balík: qiime (1.8.0+dfsg-4ubuntu1)

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.

Ostatné balíky súvisiace s balíkom qiime

  • závisí
  • odporúča
  • navrhuje
  • dep: fasttree
    phylogenetic trees from alignments of nucleotide or protein sequences
  • dep: king
    interactive system for three-dimensional vector graphics
  • dep: libc6 (>= 2.15)
    GNU C Library: Shared libraries
    tiež virtuálny balík poskytovaný balíkom libc6-udeb
  • dep: libffi6 (>= 3.0.4)
    Foreign Function Interface library runtime
  • dep: libgmp10
    Multiprecision arithmetic library
  • dep: libjs-jquery
    JavaScript library for dynamic web applications
  • dep: pynast (>= 1.2.2)
    alignment of short DNA sequences
  • dep: python (<< 2.8)
    interactive high-level object-oriented language (default version)
    dep: python (>= 2.7)
  • dep: python-biom-format (>= 1.2.0)
    Biological Observation Matrix (BIOM) format (Python 2)
  • dep: python-cogent (>= 1.5.3)
    framework for genomic biology
  • dep: python-matplotlib
    Python based plotting system in a style similar to Matlab
  • dep: python-numpy
    Numerical Python adds a fast array facility to the Python language
  • dep: python-qcli
    separated module of pyqi needed for QIIME package
  • rec: ampliconnoise
    removal of noise from 454 sequenced PCR amplicons
  • rec: blast2
    transitional dummy package to ncbi-blast+-legacy
    alebo blast+-legacy
    Balík nie je dostupný
  • rec: cd-hit
    suite of programs designed to quickly group sequences
  • rec: chimeraslayer
    detects likely chimeras in PCR amplified DNA
  • rec: clearcut
    extremely efficient phylogenetic tree reconstruction
  • rec: infernal
    inference of RNA secondary structural alignments
  • rec: muscle
    Multiple alignment program of protein sequences
  • rec: parsinsert
    Parsimonious Insertion of unclassified sequences into phylogenetic trees
  • rec: python-mpi4py
    bindings of the Message Passing Interface (MPI) standard
  • rec: qiime-data
    Quantitative Insights Into Microbial Ecology (supporting data)
  • rec: r-cran-optparse
    GNU/R Command line option parser
  • sug: cytoscape
    Balík nie je dostupný
  • sug: emperor
    Balík nie je dostupný
  • sug: rdp-classifier
    extensible sequence classifier for fungal lsu, bacterial and archaeal 16s
  • sug: t-coffee
    Multiple Sequence Alignment
  • sug: torque-client
    Balík nie je dostupný

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