Software

bkgd

bkgd is a program for calculating B values across the genome. A B value is an estimate of the effect of background selection at a given site in the genome, given the recombination rate and density of sites under purifying selection.

Paper GitHub

WASP

WASP is a software package for unbiased allele-specific read mapping and molecular QTL discovery written by Bryce van de Geijn and Graham McVicker.

Paper GitHub

genome

genome is a python library for working with genomics data. It contains code for reading / writing HDF5 files that is based loosely on Michael Hoffman's genomedata format.

GitHub

draw_genes

draw_genes is a program for plotting genomics data that is in HDF5 format. This code was used to generate figures for several papers including panels B & C of this figure; panel D of this figure; and panel B of this figure.

GitHub

check_fastq

check_fastq is a tool for checking and repairing fastq files.

GitHub