Sharcgs

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Description

sharcgs website  

SHARCGS - SHort-read Assembler based on Robust Contig-extension for Genomic Sequencing.

SHARCGS generates long contigs of genomic sequence based on very short 25-40mer, error prone reads as produced by 2nd generation sequencing machines. A large number of equal-sized reads is read from the input file and concatenated to generate contigs of several 1000 bases in length. The reads may contain errors in as many as 2% of all base calls.

Required Modules

Serial

  • sharcgs

System Variables

  • HPC_SHARCGS_DIR
  • HPC_SHARCGS_DATA -- Sample data directory




Citation

If you publish research that uses sharcgs you have to cite it as follows: Dohm JC, Lottaz C, Borodina T, Himmelbauer H. 2007. SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. Genome Res. 17: 1697-1706


Validation

  • Validated 4/5/2018