readme

README.md

@@ -0,0 +1,87 @@
+
+#SiLiCO: Simulator of Long Read Sequencing in PacBio and Oxford Nanopore 
+
+
+###Installation
+---
+If you've downloaded the source code, unpack SiLiCO, build, and install it.
+
++ `tar -xvzf SiLiCO-1.0.0.tar.gz`
++ `cd SiLiCO-1.0.0`
++ `python setup.py build`
++ `python setup.py install`
+
+###Requirements
+---
+SiLiCO is compatible with Python 2.7.11 or higher and Python 3.5 or higher.
+
+SiLiCO requires the following dependencies, which are installed during setup:
+
++ [numpy](http://www.numpy.org/)
++ [pybedtools](https://pythonhosted.org/pybedtools/)*
++ [natsort](http://pythonhosted.org/natsort/)
+
+*pybedtools relies on the pysam package. The latest version of pysam (0.9.1.3) is problematic on OS X systems. SiLiCO installs pysam v.0.8.4, to avoid this, but installing other packages that install pysam may update it to the latest version. If you encounter a `Symbol not found: _hfile_plugin_init_libcurl` error when running SiLiCO, downgrade pysam with `pip install pysam==0.8.4`. 
+
+
+
+
+###Usage Instructions
+---
+
+```
+python SiLiCO.py -i </path/to/genome> [-o </path/to/outDir> -m <mean read length> -s <standard dev of read lengths> -c <coverage> -t <trials> -f]
+
+[ FILE I/O ]
+
+-i, --infile=<str>, REQ			Input genome fasta file. See README for formatting requirments**.
+-o, --output=<str>, OPT			Output directory for results. Default = Current directory
+
+[ DISTRIBUTION PARAMETERS ]
+
+-m, --mean_read_length=<int>, OPT	Mean read length for in-silico read generation. Default = 10000 bp
+-s, --standard_dev=<int>, OPT		Standard deviation of in-silico reads. Default = 2050
+-c, --coverage=<int>, OPT		Desired genome coverage of in-silico sequencing. Default = 8
+--trials=<int>, OPT			Number of trials. Default = 1 
+
+[ MODES ] 
+
+-f, --fasta, OPT 			FASTA Mode. When present, converts bed files to FASTA sequences using the provided reference genome.
+-n, --nanopore, OPT 		Generate Oxford Nanopore data. Calculates a gamma distribution.
+-p, --pacbio, OPT 			Generate PacBio data. Calculates a log normal distribution. Default mode if none specified.
+
+[ DOCUMENTATION ] 
+
+-h, --help				Display this message.
+--version				What version of SiLiCO are you using?
+--contact				Report a bug or get more help.
+--citation				View the citation for SiLiCO.
+```
+---
+###Formatting Requirements
+
+---
+Input genome fasta should ideally be a chromosomal assembly with header lines in the style >chr1, >chr2.
+
+
+###About SiLiCO
+---
+
+If you use SiLiCO in your research please cite it as follows: 
+
+[Citation Placeholder]:
+
+`Ethan Alexander Garcia Baker, Mendivil Ramos, O., McCombie, W.R., "SiLiCO:A Simulator for Long Read Sequencing in PacBio and Oxford Nanopore". Bioinformatics. [Date]`
+
+SiLiCO is made freely available under the GNU GPL 3.0 license.
+This software may be freely modified and (re)distributed, but you must make your modifications freely available and cite SiLiCO.
+
+View LICENSE.txt or [http://choosealicense.com/licenses/gpl-3.0/](http://choosealicense.com/licenses/gpl-3.0/) for more information.
+
+---
+
+(c) 2016 Ethan Alexander García Baker
+
+<img src="https://www.cshl.edu/images/stories/about_us/logos/cshllogo_standard_RGB.png" alt="cshl logo" width="259"> 
+
+![pitt_logo](http://www.communications.pitt.edu/images/shared/pitt.gif)