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 JC, Lottaz C, Borodina T, Himmelbauer H SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing. Genome Research 2007 17: 1697-1706.

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

Dohm JC, Lottaz C, Borodina T, Himmelbauer H Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res. 2008 Jul 26.[Epub ahead of print]<!-- END INCLUDE -->

Categories

biology, ngs, de_novo