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Module Overview
FACET consists of five modules that perform different functions.
Each module has at least one 'alias' that can be used to direct FACET to that module
(e.g., the database module can be called using FACET database OR FACET db).
The database module creates a BLAST database, searches the database, and outputs BLAST alignments at the
user's desired level of cleanliness in a variety of file formats. Creating a database has the advantage of
being able to use BLAST's --num_threads flag, which can significantly speed up larger searches.
This is the module I usually use when doing genome x genome comparisons.
Usage: FACET database <subject.fasta> <query.fasta> [options]
Acceptable Module Aliases: database, db
The database_free module performs similar functions to the database module, but utilizes BLAST's
-subject flag instead of the -db flag. This bypasses database creation, making the program generate
fewer files. This is the module I usually use when doing small searches
(i.e., a fungal genome as the subject and a few transposons as the query).
Usage: FACET db_free <subject.fasta> <query.fasta> [options]
Acceptable Module Aliases: db_free, dbf, database_free
The outfile module performs similar functions to the database and database_free modules, but operates
on output files from BLASTn or FACET (.csv). This module requires the subject and query fasta files that were used to
generate the output file so that FACET can output different filetypes. This can be a very useful module if there is a
BLAST search that takes an extremely long time, as the output can be stored in a file and operated on later.
Usage: FACET outfile <blastn.out> <subject.fasta> <query.fasta> [options]
Acceptable Module Aliases: outfile , o
The masker module performs a genome self-comparison using BLASTn and utilizes self-alignments to mask
repetitive regions in a provided genome.
Usage: FACET masker <genome.fasta> [options]
Acceptable Module Aliases: masker, m
the vc module takes a VCF file and a genome file as input. It performs a genome self-comparison using BLASTn and
utilizes self-alignments to identify variants that are called in repetitive regions of the genome.
Usage: FACET vc <mpileup.vcf> <genome.fasta> [options]
Acceptable Module Aliases: vc, vcf, v