In species where the reference genome or annotation is incomplete, RNA-Seq analyses can benefit from performing a genome-guided and de novo assembly, in addition to using the reference annotation. Necklace is a software pipeline to run genome-guided and de novo assembly and combine the resulting transcriptomes with reference genome annotations. Necklace constructs a compact but comprehensive superTranscriptome
module spider necklace to find out what environment modules are available for this application.
- HPC_NECKLACE_DIR - installation directory
- HPC_NECKLACE_BIN - executable directory
- HPC_NECKLACE_CONF - installation directory
Make sure to use HPC_NECKLACE_CONF to point the software to the necklace.groovy file.