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Velvet

Description

velvet website

Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD

We provide velveth and velvetg executables built with several different kmer lengths and OMP support:

velveth, velvetg - MAXKMERLENGTH=31. velveth_max99, velvetg_max99 - MAXKMERLENGTH=99. velveth_OMP, velvetg_OMP - MAXKMERLENGTH=31, OpenMP support. velveth_max99_OMP, velvetg_max99_OMP - MAXKMERLENGTH=99, OpenMP support. velveth_de, velvetg_de - MAXKMERLENGTH=31, color support (454).

Environment Modules

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

Environment Variables

  • HPC_VELVET_DIR - installation directory
  • HPC_VELVET_BIN - executable directory
  • HPC_VELVET_EX - example data directory
  • HPC_VELVET_DOC - documentation directory
  • HPC_VELVET_CONTRIB - contributed scripts directory

Additional Usage Information

  1. If you use one of the OpenMP versions of velvet, you must set the enviroment variables OMP_NUM_THREADS and OMP_THREAD_LIMIT to the appropriate value based on the processor request in your submission script. For example if you use #PBS -l nodes=1:ppn=8 in your script, also include export OMP_NUM_THREADS=7; export OMP_THREAD_LIMIT=8 (for a bash script) in the script itself
  2. Please file a bugzilla request if you need an executable with different compile-time options such as color space, different kmers, LONGSEQUENCES, etc.

Categories

biology, genomics