Project Plan

Date	Analysis	Software	Run time	Cores	Status
May 6	Reads Quality Control	FastQC	~1-10 min/file	1	Completed
May 6	Reads Preprocessing	Trimmomatic	~0.5 min/file	2	Completed
July 29	DNA Assembly	SPAdes	~12 h	12	Completed
July 29	DNA Assembly	SOAPdenovo	~1.5 h	4	Completed
July 29	GapCloser	SOAPdenovo	~25 h	4	Completed
July 31	RNA Assembly	Trinity	~4 h	2	Completed
August 7	DNA Assembly Validation	MUMmerplot	SPAdes: ~3 h SOAPdenovo: ~10 min	2	Completed
August 12	Annotation	Maker2	Maker2 Round 1: ~1 h Post SNAP Maker run: ~30 min Post AUGUSTUS Maker Run: ~1 h	4	Completed
August 13	Aligner	TopHat	WGS Reads: ~1 h/file	2	Completed
August 15	Differential Expression	BamSort HTSeq DESeq2	10 min	1	Completed