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SHARCGS

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.

Environment Modules

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

Environment Variables

  • HPC_SHARCGS_DIR - installation directory
  • HPC_SHARCGS_DATA - Sample data directory

Citation

If you use the programs or Helicobacter Solexa data for a publication please cite:

Dohm, J. C., Lottaz, C., Borodina, T., & Himmelbauer, H. (2007). SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. Genome Research, 17(11), 1697-1706. https://doi.org/10.1101/gr.6435207

If you use Beta vulgaris Solexa data for a publication please cite:

Dohm, J. C., Lottaz, C., Borodina, T., & Himmelbauer, H. (2008). Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Research, 36(16), e105. https://doi.org/10.1093/nar/gkn425

Categories

biology, ngs, de_novo