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necklace website  

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

Environment Modules

Run module spider necklace to find out what environment modules are available for this application.

System Variables

  • HPC_NECKLACE_DIR - installation directory
  • HPC_NECKLACE_BIN - executable directory
  • HPC_NECKLACE_CONF - installation directory

Additional Information

Make sure to use HPC_NECKLACE_CONF to point the software to the necklace.groovy file.