Issues

• kaiju2table does not add superkingdom

  bioinformatics-centre/kaiju#302 · Filter by author Manso002 opened on Jun 1, 2026
  1

• Kaiju fails to find the right matches with very large custom database - large scale problem during indexing?

  bioinformatics-centre/kaiju#301 · Filter by author m-kluge opened on Feb 19, 2026
  2

• Clarification on build dates for pre-compiled databases

  bioinformatics-centre/kaiju#298 · Filter by author HenryCarr98 opened on Oct 10, 2025
  4

• http://kaiju.binf.ku.dk/ doesn't work

  bioinformatics-centre/kaiju#297 · Filter by author vivekbibs opened on Jul 24, 2025
  3

• huge false positive ratio

  bioinformatics-centre/kaiju#296 · Filter by author farhadm1990 opened on Jun 10, 2025

• Inconsistency in -u argument

  bioinformatics-centre/kaiju#294 · Filter by author bernt-matthias opened on Apr 11, 2025
  1

• Quotes in species names

  bioinformatics-centre/kaiju#293 · Filter by author mromanov2001 opened on Mar 19, 2025

• Inspection of taxons included in the nr_euk database

  bioinformatics-centre/kaiju#292 · Filter by author rhodacyleung opened on Feb 21, 2025

• Segmentation Fault with NR Database (130GB) on WSL

  bioinformatics-centre/kaiju#291 · Filter by author Raviteja-gajula opened on Feb 11, 2025
  2

• adiitional field in output of kaiju2table

  bioinformatics-centre/kaiju#290 · Filter by author Harpreet525 opened on Jan 4, 2025

• How to deal with classification bias while using single database and its own split version ?

  bioinformatics-centre/kaiju#289 · Filter by author airmicrobiome opened on Oct 18, 2024

• merging kraken2 and kaiju

  bioinformatics-centre/kaiju#288 · Filter by author DeaconOfBiology opened on Sep 29, 2024

• Getting Repeated Species in cell free DNA profiles

  bioinformatics-centre/kaiju#287 · Filter by author arpit20328 opened on Sep 2, 2024
  2

• No fmi file after kaiju-makedb

  bioinformatics-centre/kaiju#286 · Filter by author Tpowell7 opened on Aug 28, 2024
  3

• kaiju2table taxonomic ranks for viruses

  bioinformatics-centre/kaiju#283 · Filter by author jbergt opened on May 28, 2024

• Not able to download any kaiju_database from https://bioinformatics-centre.github.io/kaiju/downloads.html

  bioinformatics-centre/kaiju#282 · Filter by author arpit20328 opened on May 10, 2024

• kaiju-mergeOutputs for merging all kaiju outputs from different databases

  bioinformatics-centre/kaiju#279 · Filter by author EorgeKit opened on Feb 20, 2024
  2

• Fungal reads - Which is the best database?

  bioinformatics-centre/kaiju#278 · Filter by author andressamv opened on Feb 5, 2024
  1

• Segmentation fault (core dumped)

  bioinformatics-centre/kaiju#277 · Filter by author DoreenAA2023 opened on Jan 6, 2024
  4

• makedb progenomes fails

  bioinformatics-centre/kaiju#273 · Filter by author Mewgia opened on Nov 23, 2023
  9

• more than 73% is unclassified.

  bioinformatics-centre/kaiju#271 · Filter by author jojyjohn28 opened on Oct 17, 2023
  2

• Read classification using database of single pangenome

  bioinformatics-centre/kaiju#267 · Filter by author snayfach opened on Jul 23, 2023

• Issue with extracting taxdump

  bioinformatics-centre/kaiju#266 · Filter by author Mayurk619 opened on Jul 4, 2023
  1

• Unable to Find Taxon_ID of the Top-hit Species in Kaiju Output File Despite Being the Highest-Reads Species in Kaiju2table Output

  bioinformatics-centre/kaiju#265 · Filter by author SenyuanGu opened on Jun 29, 2023
  4

• converting kaiju output to biom format

  bioinformatics-centre/kaiju#264 · Filter by author najoshi opened on Jun 16, 2023