QUICKSCAN(1) OGMP SEQUENCE UTILITIES QUICKSCAN(1) NAME read2phrap - create an sequence assembly with phred/phrap/consed suite of tools SYNOPSIS read2phrap [OPTIONS] DESCRIPTION read2phrap has been derived from the popular perl script distributed with phred/phrap called "phredPhrap". Usage is almost identical, however the structure of the programme has been functionalised, and a number of additional features have been provided. read2phrap provides a simple way for a user to build a sequence assembly from a collection of scf files. The user simple require a directory called "chromat_dir" which contains their scf files, and from within this directory "read2phrap" can be executed with no additional options (however the -q option is highly recommended). Upon completion, the a number of new directories will have been created at the same directory tree level as the chromat_dir; - ace_backup - where ace files (assembly data) are archived after subsequent re-assemblies. - analysis - where personal analysis on the assembly can be stored - chromat_dir - where scf files are placed. - edit_dir - where assembly data is stored. - fix_data - where scf files with problems are placed after an assembly. - masterfile - where masterfiles are stored. - mf_backups - - new_data - where new scf files are place when new data is added to an existing assembly. - phd_dir - where the phred phd readings are stored. OPTIONS All arguments are optional. -q The value following this option should be a value between 1 and 99, indicating the percentage of quality disallowed in the sequence. For example, a value of "95" would allow disallow sequence data that had a quality percentage of less than 95. -m The value following this option is the maximum sequence length of motifs trimmed from bad quality readings. If no value is provided, the default value is 20 base pairs. -h Print the usage information -notags Do not create consensus tags (not recommended) -exclude_chromats exclude_chromats must be followed by the name of the file containing the chromats to exclude from the assembly. -include_phds include_phds must be followed by the name of the file containing the phd files to include in the assembly. -file_with_new_ace_file_name file_with_new_ace_file_name must be followed by the name of the file of the new ace file to be created. -ace_file_with_consensus_tags ace_file_with_consensus_tags must be followed by the name of the file that contains the consensus tags. read2phrap as accepts any options that "phrap" would normally take. Please see the "phrap" man documenation for details. SEE ALSO phred(1), fasta(1), scf2scf(1) Phrap (http://http://www.phrap.org/) VERSION 1.0 AUTHOR David To, March, 2005 Franz Lang (Project Management)