Example Usage

An example usage of the extract subcommand to extract records from a FASTA file based on a list of k-mers and their reverse complements is shown below. Records from input.fasta matching any of the k-mers in query_kmers.txt are written to the file output.fasta. Logging information is written to the terminal (stdout):

merkurio extract -i input.fasta -o output.fasta -f query_kmers.txt -r -l

Another example where paired-end reads are extracted if they contain the sequence ACGT or TGCA; the extracted records are printed to the terminal and logging information is written to two files; as plain text to log.txt, and in JSON format to log.json:

merkurio extract -1 in_R1.fastq -2 in_R2.fastq -o output -s ACGT TGCA -l log.txt -j log.json

The following example only writes the matching statistics to a JSON file log.json; FASTA output is suppressed:

merkurio extract -i input.fasta -f query_kmers.txt -S -j log.json