CATS-rf requires a transcriptome assembly in FASTA format, along with short RNA-seq reads used during assembly in either FASTQ or FASTA format. Compressed (.gz) read files are supported.
CATS-rf supports both paired-end and single-end library configurations.
Example paired-end mode usage:
CATS_rf [OPTIONS] TRANSCRIPTOME READS1 READS2
Example single-end mode usage:
CATS_rf -C se -m MEAN_INS_SIZE -s SD_INS_SIZE [OTHER_OPTIONS] TRANSCRIPTOME READS1
Single-end mode requires three options to be specified: C for library configuration, m for mean fragment size, and s for standard deviation of fragment size. Note that single-end runs will output only general assembly statistics, read mapping metrics, and positional coverage and accuracy analysis.