5.0.0 - 2026-06-14

Release Notes

Added

• Kractor now supports reading FASTA as input. The input format (FASTA or FASTQ) is detected from the first record, so no flag is needed to specify it. Output format defaults to the same as the output format (fastq outputs fastq, fasta outputs fasta unless specified otherwise - see below)
• --output-format option to choose the output sequence format. Takes auto (the default - match whatever the input
  was), fasta, or fastq. This replaces the old --output-fasta flag.

Changed

• Switched the FASTX parsing backend from noodles to needletail.
• Renamed several fields in the JSON summary to be clearer and more consistent:
  • taxons_identified -> matched_taxon_ids
  • reads_extracted_per_taxon -> assigned_reads_per_taxon
  • total_reads_in -> total_input_records
  • total_reads_out -> total_output_records
  • proportion_extracted -> extraction_fraction
  • input_format -> input_sequence_format
  • output_format -> output_sequence_format
  • missing_taxon_ids -> requested_taxon_ids_not_found
• The summary now also reports the taxon IDs you asked for in requested_taxon_ids, and whether the input was paired or
  single in input_layout.
• Migrated to the Rust 2024 edition.

Removed

• --output-fasta flag. Use --output-format fasta instead.
• noodles dependency, replaced by needletail.

Fixed

• Prevent a panic when -i/-o were passed without a file path - they now require at least one argument.
• No longer store the length and LCA fields when parsing the kraken output, since they were never used.
• Typo in the --compression-format help text.

Download kractor 5.0.0

File	Platform	Checksum
kractor-aarch64-apple-darwin.tar.xz	Apple Silicon macOS	checksum
kractor-x86_64-apple-darwin.tar.xz	Intel macOS	checksum
kractor-x86_64-unknown-linux-gnu.tar.xz	x64 Linux	checksum

kractor-4.0.0

[4.0.0] - 2026-01-26

Changed

• Summary output now lists identified taxon IDs in taxons_identified (replacing total_taxon_count)
• Summary output now includes zero entries for identified taxa with no direct assignments in reads_extracted_per_taxon

kractor-3.1.0

[3.1.0] - 2025-12-12

Added

• Attempt to detect headers in kraken report files and skip if it looks like a header. It does this by checking if there
  are 6 fields that are all strings (or more precisely if each field returns an error when parsing into an int/float).
  If so, it is assumed that this line is a header and is skipped. A warning message is printed in this case.
• --no-header-detect flag to force parsing Kraken reports from the first line without auto-skipping headers, disabling the new header detection behavior described above

Changed

• Kraken report/output parsing errors now include the line number and o line for easier debugging.

kractor-3.0.1

[3.0.1] - 2025-10-16

Fixed

• Prevent a panic when writing to output paths without an extension.

kractor-3.0.0

[3.0.0] - 2025-09-26

Added

• Able to specifiy taxon ids that are not present, without kractor stopping. These are instead logged to stderr with a warning. This may be useful when running kractor in a wrapper script for several fastq files and just want to extract a set of taxonids from them all - without caring if they are present or not #31.
• Include a new field missing_taxon_ids in the summary output.

Changed

• Under the hood refactoring, introducing structs for the processed kraken outputs and processed kraken trees to simplify the returned data.

Fixed

• Unclassified reads being skipped in the tree building stage, meaning they were unable to be extracted #30

kractor-2.0.0

[2.0.0] - 2025-08-12

Added

• Added a reads_extracted_per_taxon field to to summary report (#28)
• Added a proportion_extracted field to summary report (#28)
• Added the version to summary report (#28)
• Added an output format (fasta or fastq) field to the summary report (#28)
• Added a --verbose flag (in addition to the existing -v)

Changed

• Removed -O for compression type, now uses --compression-format for clarity.
• Removed -l for compression level, now uses --compression-level for clarity.
• Renamed --json-report to --summary
• Improved the JSON report format to make it easier to read by removing Paired and Single fields and instead having a simple total_reads_in and total_reads_out field.

Fixed

• Removed duplicate log message for taxon IDs identified
• Clippy warnings

kractor-1.0.1

[1.0.1] - 2025-06-28

Fixed

• Create subdirectories specified in output path if they don't exist (#24)
• Add output validation to prevent overwriting existing files (#25)

kractor-1.0.0

docs: changelog

v0.4.0

0.4.0

• rename to kractor
• json report output upon completion #6
• minor optimisations

Full Changelog: v0.3.0...v0.4.0

v0.3.0

0.3.0 (#11)

• Support for paired-end files #12
• Under the hood changes to use Niffler/Noodles for fastq parsing and compression #10
• Steamline arguments related to compression outputs #7 #9
• Output a fasta file --output-fasta #13
• Improved logging