Standalone package of Genotrick
Installation
- 1. After downloading the Genotrick.tar.gz package, user shouls extract it by the command tar -zxvf Genotrick.tar.gz.
- 2. Run the perl program install.pl and provide the path for the installation of Genotrick.
- 3. After installation, all perl programs and corresponding configuration files (i.e. config_file_ALL, config_file_filter, config_file_assemble, Genotrick_filter.pl, Genotrick_assemble.pl, Genotrick_annotate.pl and Genotrick_ALL.pl) will be available in bin directory.
Usases
- 1. Filtering of whole genome sequencing data :- perl Genotrick_filter.pl config_file_filter
- 2. Whole genome assembly :- perl Genotrick_assemble.pl config_file_assemble
- 3. Prokaryotic genome annotation :- perl Genotrick_annotate.pl contig.fasta (contig file)
- 4. Complete Genotrick (Whole genome assembly and annotation from raw sequencing data) :-perl Genotrick_ALL.pl config_file_ALL
Dependencies
Standalone package of Genotrick pipeline is freely avilable for scientific community. It is a user friendly package and anybody can downloa d and install standalone package of Genotrick pipeline from this webpage. Genotrick has several dependencies and follows :
Requirements
- GD::Graph perl module (optional, used to prepare graphs)
- String::Approx perl module (required to speed up the string matching for primer/adapter)
- BioPerl >= 1.6.2 (was 1.6.0)
- BLAST+ >= 2.2
- HMMer >= 3.1
- Aragorn >= 1.0
- Prodigal >= 2.0
- tbl2asn >= 21.0
- GNU Parallel >= 20130422 (was 20120322)
Recommended
- Barrnap >= 0.1 (fast rRNA searching using NHMMER)
- MINCED => 0.1.4 (find CRISPRs)
- Infernal >= 1.1rc (for --rfam / non-coding RNA predictions))
Optional
- RNAmmer >= 1.2 (requires patch to ensure it uses older HMMer 2.x)
- HMMer >= 2.0 (for RNAmmer)
- SignalP >= 3.0 (for --gram / sig_peptide predictions)