TreeToReads 0.0.3

Tree to Reads - A python script to to read a tree, resolve polytomies, generate mutations and simulate NGS reads.

#TreeToReads

Simulation pipeline to generate next generation sequencing reads from realistic phylogenies.
Can be used to test effects of model of evolution, rates of evolution,
genomic distribution of mutations, and phylogenetic relatedness of samples and of reference genome
on SNP calling and evolutionary inference.

Inputs are a phylogeny, a genome to be used as a tip in the tree,
and a set of configuration parameters in a control file

Optional inputs can include a sequencing error model parameterized from empirical data,
and a distribution for the distances separating pairs of mutations in the genome.

Outputs are mutated genomes representing all tips in the phylogeny,
and simulated whole genome sequencing reads representing those genomes.
These are are useful for testing and comparison of analysis pipelines.
Mutations are currently only single nucleotide variants - no indels or rearrangements.

The code is still in development - but testing welcome, and will be supported via email ejmctavish, gmail.

##Requirements:

- Seq-Gen
- Art

(can be run without Art if you want to generate mutated genomes, but not reads)
- Samtools (to output sorted bam files instead of sam)

python packages
- Dendropy


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##To install requirements
###Install Dendropy

pip2 dendropy

##### Install seq-gen, software to simulate mutations (http://tree.bio.ed.ac.uk/software/seqgen/)
on ubuntu using apt-get:

sudo apt-get install seq-gen

on Mac or linux (using homebrew, http://brew.sh/):

brew install seq-gen


##### Art and Samtools are optional, but are required to generate reads from simulated genomes
##### Install ART, software to generate short reads from simulated genomes (http://www.niehs.nih.gov/research/resources/software/biostatistics/art/)

on ubuntu using apt-get:

wget http://www.niehs.nih.gov/research/resources/assets/docs/artbinvanillaicecream031114linux64tgz.tgz
tar -xzvf artbinvanillaicecream031114linux64tgz.tgz

add art_illumina to path (see http://askubuntu.com/questions/60218/how-to-add-a-directory-to-my-path)

on Mac or linux (using homebrew):

brew install art

##### Install samtools, to generate sorted bam files from sam files (and save disk space) (http://www.htslib.org/)

on ubuntu using apt-get:

apt-get install samtools

on Mac or linux (using homebrew):

brew install samtools

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##Running the simulations (quick version):

git clone https://github.com/snacktavish/TreeToReads.git
cd TreeToReads
python treetoreads.py seqsim.cfg

Edit config file, seqsim.cfg, to fit your data.
The script by default look for a file called 'seqsim.cfg'
or first argument can be the path to a control file with any name.

Currently only runs art_illumina and generates paired end illumina data.
Alternatively, genomes can be generated, and ART run separately using any chosen parameters.

### [Full Tutorial](https://github.com/snacktavish/TreeToReads/blob/master/docs/tutorial.md)

---------------------------------------------------------
##Expected output
The script print out the parameter values and some other useful info.
If it runs successfully it will end with
"TreeToReads completed successfully!"

The output files will be in the the output directory specified in the
seqsim.cfg file, e.g. example_out
and will consist of:

##Key files
seqeunce names are prefixed by 'sim_'
fasta_files - a folder containing the simulated genomes for each tip in the tree
fastq - folder containing folders with the names of each tip from the simulation tree, in each of these folders is the gziped simulated fastq.
mutsites.txt - unordered list of the locations of mutations in the genome

###Other files generated by analysis (mostly useless)
analysis_configuration.cfg - a copy of the control file used for the analysis
seqgen.out - output messages form the seq-gen software
simtree.tre.bu - a backup copy of the tree
simtree.tre - the tree used for simulations: reformatted and polytomies randomly resolved with 0 length branches
analysis.sh - the bash commands run by the analysis
These folders contain the simulated read in fastq format
seqs_sim.txt - an intermediate file used for generating variable sites
SNPmatrix - a file in format SEQUENCE, BASE, POSITION describing all variable sites in the genome
art_log - log messages from ART software

###Docker container
TreeToReads is also available as a [Docker](https://www.docker.com/) container:

docker pull snacktavish/treetoreads
docker run snacktavish/treetoreads seqsim.cfg

to run the default example, or

docker run -v /an/example/path:/a/container/path snacktavish/treetoreads /a/container/path/my_treetoreads_config.cfg

to run on real data, where ```/an/example/path/``` contains the file ```my_treetoreads_config.cfg```.

(See the [Docker manual](http://docs.docker.com/engine/reference/run/#volume-shared-filesystems) for more information about mounting host directories in the container.)


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### Citations
This tool relies on Dendropy, ART, and Seqgen.
Please cite them (as well as this repo) in any published work using this simulation pipeline (appropriate citations below)

McTavish E. J., Timme R, (2015) Tree To Reads. https://github.com/snacktavish/TreeToReads

Huang W., Li L, Myers J. R., Marth G. T. (2012). ART: a next-generation sequencing read simulator, Bioinformatics 28 (4): 593-594

Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-9

Rambaut A. and Grassly N. C. (1997) Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13: 235-238

Sukumaran, J. and Mark T. Holder. 2010. DendroPy: A Python library for phylogenetic computing. Bioinformatics 26: 1569-1571.