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https://github.com/sandialabs/tiger
Target / Integrative Genetic Element Retriever: precisely maps IGEs (a defined type of genomic island) in bacterial and archaeal genomes; package also includes orthogonal program Islander
https://github.com/sandialabs/tiger
bioinformatics perl scr-1633 scr-2281 snl-other
Last synced: about 1 month ago
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Target / Integrative Genetic Element Retriever: precisely maps IGEs (a defined type of genomic island) in bacterial and archaeal genomes; package also includes orthogonal program Islander
- Host: GitHub
- URL: https://github.com/sandialabs/tiger
- Owner: sandialabs
- License: other
- Created: 2019-11-20T20:45:57.000Z (about 5 years ago)
- Default Branch: master
- Last Pushed: 2024-10-29T21:13:08.000Z (about 2 months ago)
- Last Synced: 2024-10-30T00:58:08.607Z (about 2 months ago)
- Topics: bioinformatics, perl, scr-1633, scr-2281, snl-other
- Language: Perl
- Homepage:
- Size: 45.3 MB
- Stars: 10
- Watchers: 4
- Forks: 4
- Open Issues: 4
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# TIGER version 2
Target / Integrative Genetic Element Retriever, version 2
# Citation
Mageeney CM, Lau BY, Wagner JW, Hudson CM, Schoeniger JS, Krishnakumar R and Williams KP. 2020. New candidates for regulated gene integrity revealed through precise mapping of integrative genetic elements. Nucleic Acids Research 48(8):4052-4065 (doi.org/10.1093/nar/gkaa156)
Mageeney CM, Trubl G, Williams KP. 2022. Improved mobilome delineation in fragmented genomes. Front Bioinform doi: 10.3389/fbinf.2022.866850
# INSTALLATION
git clone -b TIGER2 https://github.com/sandialabs/TIGER.git
User should have a reference genome blast database available, such as refseq_genomic
User should download Pfam-A.hmm from pfam and place it or a symbolic link to it in the TIGERPATH/db directory
```ln -s /ABSOLUTE_PATH/Pfam-A.hmm PATH_TO_TIGER/db/Pfam-A.hmm```
The following programs (with suggested versions) must be properly installed and in the user's path:
* blastn, blastdbcmd, makeblastdb 2.6.0+
* prokka 1.11
* bedtools 2.27.1
* tRNAscan-SE 2.0.2
* cmscan 1.1.2
* Perl Core: List::Util, File::Spec, Cwd, Getopt::Long
* Perl Noncore: IPC::Run3
# RUNNING
Requires a .fa file in the same folder with the same prefix.
You may add a .tax file to specify what the genome is.
The tab-separated fields of the one-line .tax file are:
1. taxid
2. organism
3. Division;Phylum;Class;Order;Family;Genus;Species
4. Genetic code (see https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi)
5. Nickname (short name for organism, eg Eco837 for the 837th E. coli genome)
## Sample calls to try within /testdata (PATH: to TIGER installation; DB: to reference genome blast database)
```perl PATH/bin/islander.pl -verbose genome.fa &> islander.log```
```perl PATH/bin/tiger.pl -verbose -db DB -cross simple -fasta genome.fa &> tiger.log```
```perl PATH/bin/resolve.pl mixed lenient genome genome.island.merge.gff islander.gff &> resolve.log```
```perl PATH/bin/typing.pl resolved.gff &> typing.log```
```perl PATH/bin/typing.pl genome.island.nonoverlap.gff &> typing.log```
## Notes:
before rerunning islander.pl: ```rm genome.stats```
before rerunning tiger.pl: ```rm genome.island.nonoverlap.gff```