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##merge2files

Script to compare and merge two files based on user specified matched columns. for usage: merge2files.pl -h

##runVirusdetection

  • Tool to detect virus or bacterial sequences in sequenced samples using GOTTCHA
  • Tracey Allen K. Freitas, Po-E Li, Matthew B. Scholz and Patrick S. G. Chain (2015) Accurate read-based metagenome characterization using a hierarchical suite of unique signatures, Nucleic Acids Research (DOI: 10.1093/nar/gkv180)
  • Download latest signature database for specific organism from : ftp://ftp.lanl.gov/public/genome/gottcha/GOTTCHA_database_v20150825/
  • Also needs lookup database GOTTCHA_lookup.tar.gz
  • runVirusdetection.sh

##runPathogenDetection

  • This is generic perl wrapper to detect pathogen seuences using GOTTCHA method [see above description for reference]
  • More robust options to select unmapped reads sequences