Metabuli v1.0.8

• Added extract module: It extracts reads classified under a specific taxon at any ranks. It can be used after running classify.

Metabuli v1.0.7

Metabuli became faster than v1.0.6

• Dataset

  • Query: SRR24315757_1.fastq, SRR24315757_2.fastq
    • 22,107,398 paired-end reads
    • 6,632,219,400 nt in total
  • DB: GTDB
    • Complete Genome or Chromosome level assemblies
    • CheckM completeness > 90 and contamination < 5
    • 36,203 genomes from 8,465 species

• Windows: ~8.3 times faster

  • Machine: Intel(R) Core(TM) i9-9900 CPU, 32GB RAM
  • --max-ram: 32
  • --threads: 8
  • v1.0.6: 825s for the first 587,593 reads (2.7% of all). Total time not measured
  • v1.0.7: 100s for the first 587,593 reads. 1h 7m 22s in total

• MacOS: ~1.7 times faster

  • Machine: MacBook Pro 14-inch 2023, M2 Pro chip, 32GB RAM
  • --max-ram: 32
  • --threads: 8
  • v1.0.6: 71m 34s
  • v1.0.7: 42m 58s

• Linux: ~1.3 times faster

  • Machine: A server with 64-core AMD EPYC 7742 CPU and 1 TB of RAM
  • --max-ram : 128
  • --threads : 32
    • v1.0.6: 13m 34s
    • v1.0.7: 9m 58s
  • --threads : 64
    • v1.0.6: 9m 36s
    • v1.0.7: 7m 19s

Metabuli v1.0.6

Windows OS is supported

Metabuli v1.0.5

The CMake file was edited to pass the Bioconda PR test.
Other than that it is the same as v1.0.4.

Metabuli v1.0.4

• Fixed a minor reproducibility issue.
• Fixed a performance-harming bug occurring with sequences containing lowercased bases.
• Auto adjustment of --match-per-kmer parameter. Issue #20 solved.
• Record version info. in db.parameter

Metabuli v1.0.3

• New parameter: --tie-ratio in classify module. [default 0.95]
  When the best matching species has a score MAX, species with score >= (MAX * --tie-ratio) is considered as a tie to the best score. When tie species occur for a read, the read is classified into their LCA.

Metabuli v1.0.2

v1.0.2

• --accession-level option for build and classify workflow: It reports not only the taxon but also the accession of the best match.
• Fix minor bugs in build and classify workflow.
• Generate taxonomyDB during build and load it during classify workflow for faster loading of taxonomy information.
• Support gzipped FASTA/FASTQ files in add-to-library and classify workflows.
• low-complexity filtering in build workflow as default with --mask-prob 0.9.

Metabuli v1.0.1

• Fixed memory-related bugs.
• classify generates a Krona report file.
• New option of classify: Low-complexity masking by --mask and --mask-prob (#20)
• New option of classify: --match-per-kmer option in classify workflow (#20)
• databases downloads DBs as tar.gz and unzips them.
• classify ignores reads shorter than 26 nt.
• database-report generates a report of taxa included in a database.

Metabuli v1.0.0

It is the first release of Metabuli.

Metabuli is a metagenomic classifier that jointly analyze both DNA and amino-acid sequences to achieve high specificity and sensitivity at the same time. It is implemented based on a novel k-mer structure, metamer, to efficiently index and compare sequences at both DNA and amino-acid level.