This repository contains the scripts used to construct synthetic long reads and the data to recreate the plots from Stapleton et al. 2015, "Haplotype-phased synthetic long reads from short-read sequencing."

Each of the samples described in the paper has its own directory, Chicken/ Gelsemium2/ HepG2/ MG1655/ multiplex/ Env/ Gelsemium/ HCT116/ Potato/

... which contains a makefile that will construct synthetic reads from the raw data (which can be downloaded from the Sequence Read Archive). In practice, most of these assemblies are best done on a cluster.

The python scripts called by the makefiles are in Scripts/

Figures.ipynb is an ipython notebook to recreate most of the figures in the paper.

HPCC_Hasher.sub and HPCC_Spades.sub are qsub files for running the hashing and assembly steps on a cluster.

This directory also contains JAStrim.fa and pairedTrim.txt, which are adapter files for trimmomatic.