CANDY provides a command line interface to create customized amplicon databases using in silico PCR with the specified primer sequences. CANDY will create database files that serve as input for SMORE'D, a k-mer based classification tool. The required input for this program is a tabular format file containing the primers and their accompanying metadata. Optionally, additional FASTA files containing annotated sequences to include in the generated database can be used. There are two types of sequences that may be added in the additional FASTA files, presence/absence sequences and characterization sequences. These sequences differ in the way they are reported by SMORE'D. SMORE'D reports the number of times a read matches a presence/absence sequence. Only the most abundant of the sample characterization categories is reported e.g. , if there are 10,000 Mycoplasma pneumoniae P1-type 1 sequences and 1,000 Mycoplasma pneumoniae P1-type 2, the sample is characterized as Mycoplasma pneumoniae P1-type 1 and only the read count for Mycoplasma pneumoniae P1-type 1 is reported. CANDY will output a FASTA file of representative sequences for the database, a profile file which maps the representative sequences to their annotations, and a configuration file.
candy.py –i [-o ] [-d ][-g <additional presence/absence seqs>] [-a ] [-t ] [-m ] [Bracketed arguments are optional]
-i, --input Input primer file; tab-separated, 6-column file
-o, --output_prefix Takes a string to be added to the beginning of the output files (amplicons.fasta, profile.tsv, and config.txt) -g, --pres_abs_seqs Takes a FASTA file of presence/absence sequences to be included in the database -a, --charac_seqs Takes a FASTA file of sample characterization sequences to be included in the database -d, --intermediate_dir Is the name for the directory which holds intermediate files produced. Default name is date-time -t, --threads Takes an integer argument which tells CANDY how many threads to use -m, --mapping Takes a tab-separated, 2-column annotation mapping file
-l, --log Takes a name for the log
candy.py --update -p -m
--update Tells CANDY to run in update mode -p, --profile The existing profile file to be updated -m, --mapping The updated annotation mapping file