Feature Overview

MerKurio provides two complementary subcommands:

• 🔍 Extract: Search FASTA/FASTQ data for k-mers and write records with matching k-mers to the terminal or a new file.
  • Supports paired-end reads (a hit in one read extracts the whole pair).
• 📑 Tag: Annotate BAM/SAM alignments with k-mer tags and filter them based on matching k-mers.
  • Adds a two‑letter tag (default km) with comma-separated matching k‑mers (follows the SAM format specification).
  • Optionally keeps only reads containing at least one k‑mer.
  • Multithreaded processing when working with BAM files.

Both commands share additional features:

• Records detailed matching statistics (positions of k-mer occurence, summary statistics, metadata).
  • Human readable output in plain text.
  • Structured JSON logs for easy machine parsing.
• Reads compressed input files (.gz, .bz2, .xz).
• Can seach for reverse complements or only canonical forms of k-mers.
• Case-insensitive search or conversion to lower-/uppercase.
• Inverse matching to keep only those records without matches.
• Query k-mers can be provided as command line arguments or in a file (FASTA or plain text).
• File types are inferred automatically.
• Record output can be suppressed to only record statistics.