Output formats

rkmh produces relatively simple outputs. Here we'll go through the formats produced by each command.

stream and classify

Both stream and classify produce an eight-column tab-delimited output file. The columns are as follows:

1. Read identifier
2. Reference match identifer
3. Number of matches
4. Sketch size (or min(sketch size, reference length))

Columns 5-8 are for flags which warn about potential indicators of poor classifications: 5. Number of kmers below minimum required 6. Number of matches below minimum required 7. The difference (in number of kmers) between the best and second-best matches are less than a user-defined threshold.

hpv16

The hpv16 command produces a modified version of the stream/classify output.

filter

The output of filter is fasta/fastq, based on which format the input was. Read pairing is ignored.