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github.com/DerrickWood/kraken2 @v2.17.1
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336 symbols
850 edges
43 files
26 documented · 8%
● updated 6d agov2.17.1 · 2025-11-24★ 918567 open issues
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README
Kraken 2
The second version of the Kraken taxonomic sequence classification system
Please refer to the Operating Manual (in docs/MANUAL.html) for details on
how to use Kraken 2.
Publications
For additional implementation details and guidance on using Kraken 2, you can also refer to:
- The paper describing the first version of Kraken. Note that Kraken 2 is a rewrite of Kraken 1 and is not backwards compatible with Kraken 1.
- The paper describing KrakenUniq. KrakenUniq's HLL-based functionality is incorporated in Kraken 2 when using the --report-minimizer-data flag described in the Operating Manual.
- The Kraken 2 paper.
- A protocol paper describing use of Kraken 2.
Core symbols most depended-on inside this repo
size
called by 107
src/hyperloglogplus.cc
asn1_indefinite_tag_end
called by 42
src/blast_defline.c
get_explicit_tag
called by 30
src/blast_defline.c
nodes
called by 18
src/taxonomy.h
insert
called by 17
src/hyperloglogplus.cc
asn1_get_byte
called by 13
src/blast_defline.c
alloc_memory
called by 12
src/blast_utils.c
asn1_peek_byte
called by 12
src/blast_defline.c
Shape
Languages
C++75%
C25%
Modules by API surface
src/blast_to_fasta.c45 symbols
src/hyperloglogplus.cc39 symbols
src/blast_defline.c34 symbols
src/classify.cc26 symbols
src/k2mask.cc16 symbols
src/threadpool.h13 symbols
src/libtax.cc13 symbols
src/build_db.cc13 symbols
src/seqreader.h11 symbols
src/taxonomy.cc10 symbols
src/compact_hash.h10 symbols
src/compact_hash.cc10 symbols
For agents
$ claude mcp add kraken2 \
-- python -m otcore.mcp_server <graph>