Table 1. Command line arguments for MetaCRAST.

Required arguments are in bold.

Argument	Description
-p	Pattern file containing query DR sequences in FASTA or FASTQ format
-i	Input metagenome in FASTA or FASTQ format
-o	Output directory for detected reads and spacers
-d	Allowed edit distance (insertions, deletions, or substitutions) for initial read detection with the Wu-Manber algorithm and subsequent DR detection steps
-t	Temporary directory to put metagenome parts (use this if -n option also selected)
-q	Input metagenome is a FASTQ file (directs use of fastq-splitter.pl instead of fasta-splitter.pl)
-h	Use Hamming distance metric (substitutions only - no insertions or deletions) to find direct repeat locations in reads (default: use Levenshtein distance metric - look for sequences matching DR within insertion, deletion, and/or substitution edit distance)
-r	Search for reverse complement of CRISPR direct repeat sequences
-l	Maximum spacer length in bp
-c	CD-HIT similarity threshold for clustering spacers detected for each query direct repeat (value from 0 to 1)
-a	CD-HIT similarity threshold for clustering all detected spacers (value from 0 to 1)
-n	Number of processors to use for parallel processing (and number of temporary metagenome parts)