Issues

• k2 classify with multiple database (merge) appears to not respect --minimum-hit-groups

  DerrickWood/kraken2#1044 · Filter by author fredyr opened on Sep 29, 2026
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• Release 2.17.2 appears to not been tagged correctly

  DerrickWood/kraken2#1043 · Filter by author fredyr opened on Sep 29, 2026
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• [Bug] --fast-build skips bases from multi-FASTA input when using more than one thread (v2.17.1)

  DerrickWood/kraken2#1040 · Filter by author SteamedFish6 opened on Sep 23, 2026
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• Kraken2 k2 command fails to download taxonomy and library databases

  DerrickWood/kraken2#1037 · Filter by author Qingheliuliu opened on Aug 14, 2026
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• Bug: Failing K2 merging of multi-database reports (sometimes)

  DerrickWood/kraken2#1031 · Filter by author i-sibirica opened on Jun 18, 2026
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• will you improve k2 with the similar --use-tfp function

  DerrickWood/kraken2#1024 · Filter by author Xueliang24 opened on Apr 28, 2026
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• How to use a custom database and make a validation?

  DerrickWood/kraken2#1022 · Filter by author fabriciomtza opened on Apr 20, 2026

• Which method of database construction should I use?

  DerrickWood/kraken2#1021 · Filter by author qkqk-hub opened on Apr 18, 2026

• whats the size of bacteria database is supposed to be in k2 script?

  DerrickWood/kraken2#1020 · Filter by author ciroariel opened on Apr 9, 2026

• problem with plasmid database download

  DerrickWood/kraken2#1019 · Filter by author minhasbushra opened on Apr 1, 2026
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• How to calculate the genome size or genome fasta of species in the pre-built database

  DerrickWood/kraken2#1016 · Filter by author zhangwenda0518 opened on Mar 14, 2026

• Building standard db using k2 wrapper doesn't create taxonomy folder

  DerrickWood/kraken2#1011 · Filter by author almutwerner opened on Feb 23, 2026
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• Updated advice on converting Kraken output to Biom/Phyloseq

  DerrickWood/kraken2#1009 · Filter by author fgonzalez3 opened on Jan 30, 2026
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• Using the k2 classify across multiple databases

  DerrickWood/kraken2#1008 · Filter by author Alexa2279 opened on Jan 29, 2026
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• Add genome to prebuild database

  DerrickWood/kraken2#1007 · Filter by author termithorbor opened on Jan 29, 2026
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• Pracken index file link

  DerrickWood/kraken2#1005 · Filter by author mnter opened on Jan 26, 2026
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• custome kraken2 database with thousands of genomes

  DerrickWood/kraken2#1003 · Filter by author mars188 opened on Jan 15, 2026
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• Connection timed out

  DerrickWood/kraken2#1002 · Filter by author Omicslogic-git opened on Dec 19, 2025
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• IndexError: array index out of range with latest kraken2 version (2.17.1)

  DerrickWood/kraken2#1001 · Filter by author mars188 opened on Dec 11, 2025
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• Kraken2 preferring common name for some taxa?

  DerrickWood/kraken2#1000 · Filter by author bheywar opened on Dec 9, 2025
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• Question on the results of kraken2

  DerrickWood/kraken2#997 · Filter by author erl1234 opened on Dec 5, 2025

• Feature request: make '/tmp/classify.pid' path modifyable

  DerrickWood/kraken2#996 · Filter by author Laurenz0908 opened on Nov 27, 2025

• Questions about the composition and accuracy of the Core_nt database

  DerrickWood/kraken2#995 · Filter by author nvhphuc1206 opened on Nov 11, 2025

• Build failure on macOS with v2.17

  DerrickWood/kraken2#993 · Filter by author daeho-ro opened on Nov 7, 2025
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• Kraken2 2025 prebuilt database indexes use ‘R1’, ‘R2’, etc. instead of ‘D’ for domain ranks — breaks compatibility with Pavian tool

  DerrickWood/kraken2#991 · Filter by author bhavesh-chromosomelabs opened on Oct 31, 2025
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