All pull requests

Pull requests

• Fix strip trailing slash from NCBI ftp_path to prevent malformed download URLs

  #1015·inspirewind opened Mar 9, 2026·1 task done·

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• *CRIT FIX* Create VERSION

  #934·TheWileyB opened Mar 19, 2025·

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• Parallel manifest.txt file download for rsync_from_ncbi.pl

  #890·jonathancosme opened Nov 20, 2024·

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• fix: exclude ambiguous bases from confidence scoring calculation

  #879·mcolpus opened Sep 11, 2024·

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• Interleaved Fastq input

  #843·WEClarke opened Jun 21, 2024·

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• add more deps to makefile

  #783·jchorl opened Dec 16, 2023·

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• Fix issue with Silva having domain and superkingdom taxonomic ranks both converted to superkingdom (D) in Kraken

  #745·Thomas-Bcp opened Jul 31, 2023·

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• Check existence output folder prior to running kraken2

  #718·TheOafidian opened May 9, 2023·

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• fixed library & taxonomy download functions and added multiprocessing to speed up downloads

  #698·eladc opened Mar 12, 2023·

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• Updated kraken2-build to allow symlinks in the library directory

  #603·oracle5th opened Jun 20, 2022·

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• Add batch-size option

  #586·nrhorner opened May 11, 2022·

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• Use HTTPS instead for plasmids, update path

  #529·thomcuddihy opened Nov 9, 2021·

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• Skip hash table size estimation if already done

  #450·kim-fehl opened May 16, 2021·

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• Added genbank support

  #418·d-cameron opened Feb 24, 2021·

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• Refresh FTP connection for downloading libraries with --use-ftp

  #406·tokarevvasily opened Jan 26, 2021·

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• Fix link issue with cmake

  #386·starling13 opened Dec 25, 2020·

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• Add --priority-taxids option for database building.

  #256·yesimon opened May 21, 2020·

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• Prefix auxiliary executables with kraken2_

  #91·yesimon opened Mar 4, 2019·

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• Suggestion: parallelize low complexity masking

  #39·tskir opened Aug 11, 2018·

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