CRISPRone - command line version

Warning: The command-line version of this software tool was not originally developed for public consumption, and output formats may not be in a friendly human-readable format. Command-line version is provided here to allow interested parties who may find interest in utilizing the command-line version rather than relying on the web-based server.

CRISPRone provides annotation of CRISPR—Cas systems including:

• CRISPR arrays of repeat-spacer units, and cas genes
• type (and subtype) of predicted system(s)
• anti-repeats (part of tracrRNA genes in type II CRISPR–Cas systems)

Prerequisites & Dependencies

Dependencies required to be installed prior to running CRISPRone.

    - Python 2.7+ OR Python 3.6+
    - Perl 

Usage

usage: crisprone-local.py [output-base] [output-prefix] [input-fna] <input-gff> 

required arguments:
  [output-base]   Output directory for CRISPRone results.
  [output-prefix] Prefix/label for output subdirectories and output files.
  [intput-fna]    Path to input FASTA file.

optional arguments:
  <input-gff>     Path to GFF file of intput FASTA file.

Output files of interest

output file	Description
output.crt	metaCRT output of identified CRISPRs.
output-sm.gff	GFF of CRISPR-Cas related features.
output.plot.spacer	metadata of CRISPR-Cas related features.
/spacer/all-spacer.fa	FASTA file of all identified CRISPR spacer sequences.

Citation

Quan Zhang and Yuzhen Ye. Not all predicted CRISPR-Cas systems are equal: Isolated cas genes and classes of CRISPR like elements. BMC Bioinformatics, 18:92, 2017

Acknowledgement

This work was supported by NSF grants DBI-0845685 & DBI-1262588