Example Usage

An example usage of the tag subcommand to tag a BAM file with the k-mers in the file query_kmers.fasta and output a SAM file is shown below:

merkurio tag -i input.bam -o output.sam -f query_kmers.fasta

Another example where the k-mers are provided on the command line and the search is also performed for their reverse complements. The tag is set to “MK”. BAM file processing is done with 4 threads:

merkurio tag -i input.bam -o output.bam -s ACGT TGCA -r -p 4 -t MK

This example shows how to filter the output to only include records that contain at least one of the k-mers. Output is written to the terminal (stdout):

merkurio tag -i input.bam -s AAATCAAGA -m

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

merkurio tag -i input.bam -s AAATCAAGA -S -j log.json