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High throughput sequencing analysis tools
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========== Nesoni ========== Nesoni is a high-throughput sequencing data analysis toolset, which the VBC has developed to cope with the flood of Illumina, 454, and SOLiD data now being produced. Our work is largely with bacterial genomes, and the design tradeoffs in nesoni reflect this. Nesoni focusses on analysing the alignment of reads to a reference genome. Use of the SHRiMP and Bowtie2 read aligners is automated by nesoni. We use SHRiMP as it is able to detect small insertions and deletions in addition to SNPs. Output from other aligners may be imported in SAM format. Nesoni can call a consensus of read alignments, taking care to indicate ambiguity. This can then be used in various ways: to determine the protein level changes resulting from SNPs and indels, to find differences between multiple strains, or to produce n-way comparison data suitable for phylogenetic analysis in SplitsTree4. ~ Requirements ============== Python 2.6 or higher. Use of PyPy where possible is highly recommended for performance. Python libraries * Recommended: * BioPython [1] * Optional (used by non-core nesoni tools): * matplotlib * numpy External programs: * Required: * SHRiMP or Bowtie2 * samtools * Required for VCF based variant calling: * Picard [2] * Freebayes * Optional for VCF based variant calling: * SplitsTree4 R libraries required by R-based tools (mostly for RNA-seq): * Required: * limma, edgeR from BioConductor * seriation * Optional: * goseq from BioConductor * NMF [1] BioPython is used for reading GenBank files. Compiled modules may need to be disabled when installing in PyPy. [2] There does not seem to be a standard way to install .jar files. Nesoni will search for .jar files in directories listed in environment variables $PATH and $JARPATH. ~ Installation ============== The easy way to install or upgrade: pip install -I nesoni Then type "nesoni" and follow the command to install the R module. See below for more ways to install nesoni. ~ Using nesoni ============== Type nesoni for usage instructions. nesoni can also be used without installing, from the directory in which you unpacked it: python -m nesoni ~ Advanced installation methods =============================== From source, download and untar the source tarball, then: python setup.py install Optional: R CMD INSTALL nesoni/nesoni-r For PyPy it seems to be currently easiest to install nesoni in a virtualenv: virtualenv -p pypy my-pypy-env my-pypy-env/bin/pip install -I biopython my-pypy-env/bin/pip install -I nesoni You can also set up a CPython virtualenv like this: virtualenv my-python-env my-python-env/bin/pip install -I numpy my-python-env/bin/pip install -I matplotlib my-python-env/bin/pip install -I biopython my-python-env/bin/pip install -I nesoni ~ Installing older versions =========================== The interface and API for nesoni may change between versions (I try to keep this to a minimum). In order to run a script or python program that needs an older version, I suggest setting up a virtualenv. For example, if you want version 0.95: virtualenv -p pypy my-old-env my-old-env/bin/pip install -I biopython my-old-env/bin/pip install -I nesoni==0.95 (Note: I don't have a neat way to make this work with the R components of nesoni.)
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