#####Update 5/12/2016: Construction of a new, packaged version is underway (v1)!.

#####Update 1/8/2016: This repo is under construction. I'll be pushing some usable updates soon, but they may require some adaptation to your configutations. Working on a more generalized version for the near future.

Here's a general pipeline for this code.

1. Get a reference genome/assembly by chromosome (ie. chr1.fa, chr2.fa,)
2. Generate a distribution of chromosome lengths (generate_chrdist.py)
3. simulation.py (many parameters still must be hard-coded in this draft version.) This generates a BED file of simulated reads.
4. sortBed.sh - sorts BED files by chromosome.
5. getFasta.sh - requires BEDTools, generates simulated FASTA files. This is written to be easily parallelizable.
6. (Optional, but used in AGBT presentation) countSimDimers.sh

This is a draft version of pblibsim. Your mileage may vary.