www.plantphysiol.org/content/174/3/1307
https://github.com/wacguy/Simple-1.8.1
a pipeline that takes next-generation sequencing fastq files as input...
outputs the most likely causal DNA changes. The pipeline has been validated in Arabidopsis thaliana (Arabidopsis) and can be readily applied to other species, with the possibility of mapping either dominant or recessive mutations.
operates on the input of the NGS fastq files generated from wild-type and mutant bulked DNA pools and produces tables and plots showing the most likely candidate genes and genomic locations.
