DownloadNcbiAssembly

Introduction

Example

The help menu:


Usage: DownloadNcbiAssembly [options]

  -l <value> | --log_level <value>
        Level of log information printed. Possible levels: 'debug', 'info', 'warn', 'error'
  -h | --help
        Print usage
  -v | --version
        Print version
  -a <file> | --assembly_report <file>
        refseq ID from NCBI
  -o <file> | --output <file>
        output Fasta file
  --report <file>
        where to write report from NCBI
  --nameHeader <string>

 Which column to use from the NCBI report to name the contigs.
 All columns from the report can be used but these are the most common fields to choose from:
 - 'Sequence-Name': Name of the contig within the assembly
 - 'UCSC-style-name': Name of the contig used by UCSC ( like hg19 )
 - 'RefSeq-Accn': Unique name of the contig at RefSeq (default for NCBI)
  --mustHaveOne:<key>=<column_name=regex>
        This can be used to filter based on the NCBI report, multiple conditions can be given, at least 1 should be true
  --mustNotHave:<key>=<column_name=regex>
        This can be used to filter based on the NCBI report, multiple conditions can be given, all should be false


To run the tool use:

biopet tool DownloadNcbiAssembly    

Output