First docs

README.md

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-# shovill
-Faster SPAdes assembly of Illumina reads
+# Shovill
+Faster smarter SPAdes assembly of Illumina reads
+
+## Introduction
+
+The SPAdes genome assembler has become the *de facto* standard *de novo* genome assembler
+for Illumina whole genome sequencing data of bacteria and other small microbes. SPAdes
+was a major improvement over previous assemblers like Velvet, but it can be very slow to run
+and does not handle overlapping paired-end reads well.
+
+Shovill is a pipeline which uses SPAdes at its core, but alters the steps before and after
+the primary assembly step to get near-identical results in far less time.  
+
+## Main steps
+
+1. Correct reads conservatively
+2. Pre-overlap paired-end reads
+3. Assemble with "vanilla" SPAdes with modified kmer range
+4. Correct minor assembly errors (optional)
+
+## Installation
+
+### Source
+
+```
+git clone https://github.com/tseemann/shovill.git
+./shovill/shovill -h
+```
+You will need to install all the dependencies manually:
+* SPAdes
+* Lighter
+* FLASH
+* SAMtools
+* BWA MEM
+* PILON
+* KmerStream
+
+### Homebrew
+
+**NOT READY YET**
+
+```
+brew tap homebrew/science
+brew tap tseemann/bioinformatics-linux
+brew install shovill
+```
+Using Homebrew will install all the dependencies for you.
+
+## Feedback
+
+Please file questions, bugs or ideas to the [Issue Tracker](https://github.com/tseemann/shovill/issues)
+
+## License
+
+[GPLv3](https://raw.githubusercontent.com/tseemann/shovill/master/LICENSE)
+
+## Citation
+
+Not published yet.
+
+## Authors
+
+* Torsten Seemann
+* Jason Kwong
+* Anders Goncalves da Silva
+* Mark Schultz
+* Dieter Bulach
+