KMC Database Format¶

This documentation is heavily inspired from the KMC documentation

KMC creates two files for each k-mer database:

• .kmc_pre: Contains prefix-related data and metadata.
• .kmc_suf: Contains suffixes and k-mer counters.

All integers are stored in LSB (little-endian) byte order.

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.kmc_pre File Structure¶

Contains the following sections:

1. [marker] — 4-byte string: KMCP
2. [prefixes]
3. [map]
4. [header]
5. [header position]
6. [marker] — End marker: KMCP

Header Structure ([header])¶

Field	Type	Description
kmer_length	uint32	Length of k-mers
mode	uint32	0 = count, 1 = quality-aware count
counter_size	uint32	Size of counters (1–4 bytes)
lut_prefix_length	uint32	Length of prefix removed from k-mers
signature_length	uint32	Length of k-mer signature
min_count	uint32	Minimum count threshold
max_count	uint32	Maximum count threshold
total_kmers	uint64	Total number of k-mers stored
both_strands	uchar	1 = both strands used
tmp[3]	uchar[]	Reserved
tmp[6]	uint32[]	Reserved
KMC_VER	uint32	KMC version (0x200 for KMC 2)

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Map Section ([map])¶

• Array of uint32 values.
• Size: 4^signature_length + 1
• Used to locate the proper prefixes array in [prefixes].

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Prefixes Section ([prefixes])¶

• Contains multiple arrays of uint64, one for each signature.
• Each array has size 4^lut_prefix_length.
• Followed by a guard uint64.

Used to locate k-mer suffix ranges in .kmc_suf.

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.kmc_suf File Structure¶

1. [marker] — 4-byte string: KMCS
2. [data] — Array of k-mer records
3. [marker] — End marker: KMCS

Data Section ([data])¶

• record_t records[total_kmers]
• Each record:
  • Suffix of the k-mer, packed (2 bits per base)
  • Counter value (1–4 bytes or 4-byte float)

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