FinHo

Host-Virus matches for Bacteria and Archaea

Citation

Coutinho FH, Cabello-Yeves PJ, Gonzalez-Serrano R, Rosselli R, López-Pérez M, Zemskaya TI, Zakharenko AS, Ivanov VG, and Rodriguez-Valera F. New viral biogeochemical roles revealed through metagenomic analysis of Lake Baikal. Microbiome . Microbiome; 2020;8:163.

Dependencies (must be included in the system path):

• Bioperl
• ncbi blast+
• tRNAscan-SE
• CRISPRDetect
• WIsH (Who Is the Host?)

Usage:

perl FinHo.pl - --hosts Hosts_dir/ - --phages Phage_dir/

General options:

• --format | Extension of the files containing genomic sequences in the Host and Phage directories (default = fasta)
• --threads | Number of threads to use for blast search (default = 12)
• --use_ref | Use host sequences from RefSeq instead of custom genomes
• --parse_only | Skip BLAST searches and only parse the Results (ALL the original files must be in the folder and with the same names)
• --help | Prints this message and exits.

Homology Matches options:

• --min_bitscore_hml | Minimum bitscore for considering a match (default = 0)
• --min_alignment_hml | Minimum alignment length for considering a match (default = 1000nt)
• --min_identity_hml | Minimum % identity for considering a match (default = 85%)
• --max_evalue_hml | Maximum e-value for considering a match (default = 0.001)
• --min_qcov_hml | Minimum query % coverage for considering a match (default = 0)
• --skip_hml | Flag to skip Homology Match step

RNA Matches options:

• --min_bitscore_trna | Minimum bitscore for considering a match (default = 0)
• --min_alignment_trna | Minimum alignment length for considering a match (default = 60nt)
• --min_identity_trna | Minimum % identity for considering a match (default = 95%)
• --max_evalue_trna | Maximum e-value for considering a match (default = 0.001)
• --min_qcov_trna | Minimum query % coverage for considering a match (default = 95%)
• --skip_trna | Flag to skip tRNA Match step

CRISPR Matches options:

• --min_bitscore_CRISPR | Minimum bitscore for considering a match (default = 40)
• --min_alignment_CRISPR | Minimum alignment length for considering a match (default = 0nt)
• --min_identity_CRISPR | Minimum % identity for considering a match (default = 100%)
• --max_evalue_CRISPR | Maximum e-value for considering a match (default = 1)
• --min_qcov_CRISPR | Minimum query % coverage for considering a match (default = 100%)
• --max_mismatch_CRISPR | Maximum number of mismatches for considering a match (default = 0nt)
• --skip_CRISPR | Flag to skip CRISPR Match step

WIsH options:

• --min_kmer_score | Minimum score for considering a kmer match (default = -10)
• --skip_kmer | Flag to skip Kmer search step