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