v2.1.1

• General updates for compatibility with Nextflow v26
• Added patch for countFastq error that occurs on Seqera Cloud

What's Changed

• Dev v2.1.1 by @DOH-JDJ0303 in #28

Full Changelog: v2.1.0...v2.1.1

v2.1.0

The following references were removed from the Lentivirus reference set due to significant overlap with the GRCh38.p14 human reference genome (RefSeq accession GCF_000001405.40):

• Lentivirus-wg-3825
• Lentivirus-wg-5653
• Lentivirus-wg-6651
• Lentivirus-wg-7194
• Lentivirus-wg-7734

The script used to determine this can be found here. The full output from this script is shown below:

2026-06-24 16:23:27 [INFO] epitome_filter: ======================================================================
2026-06-24 16:23:27 [INFO] epitome_filter: epitome_filter v1.0
2026-06-24 16:23:27 [INFO] epitome_filter: ======================================================================
2026-06-24 16:23:27 [INFO] epitome_filter: Configuration:
2026-06-24 16:23:27 [INFO] epitome_filter:   Inputs: 1 files
2026-06-24 16:23:27 [INFO] epitome_filter:   Output: updated.jsonl.gz
2026-06-24 16:23:27 [INFO] epitome_filter:   Target: GCF_000001405.40_GRCh38.p14_genomic.fna
2026-06-24 16:23:27 [INFO] epitome_filter:   Preset: asm20
2026-06-24 16:23:27 [INFO] epitome_filter:   Min coverage: 10.000
2026-06-24 16:23:27 [INFO] epitome_filter:   Min identity: 80.000
2026-06-24 16:23:27 [INFO] epitome_filter:   Threads: 4
2026-06-24 16:23:27 [INFO] epitome_filter: ----------------------------------------------------------------------
2026-06-24 16:23:27 [INFO] root: Loaded JSONL file: Lentivirus-wg.consensus.jsonl.gz
2026-06-24 16:23:27 [INFO] epitome_filter: Loaded 8965 records from Lentivirus-wg.consensus.jsonl.gz
2026-06-24 16:23:27 [INFO] epitome_filter: Loaded: 8965 records (8965 with sequence)
2026-06-24 16:23:27 [INFO] epitome_filter: ----------------------------------------------------------------------
2026-06-24 16:23:28 [INFO] epitome_filter: Wrote 8965 query sequences → query.fasta
2026-06-24 16:23:28 [INFO] epitome_filter: Running: minimap2 -c -x asm20 -t 4 ../GCF_000001405.40_GRCh38.p14_genomic.fna /tmp/epitome_filter_ru2kad2f/query.fasta
2026-06-24 16:24:44 [INFO] epitome_filter: ----------------------------------------------------------------------
2026-06-24 16:24:44 [INFO] epitome_filter: Evaluated 11 aligned records; 5 flagged for removal
2026-06-24 16:24:44 [INFO] epitome_filter: ----------------------------------------------------------------------
2026-06-24 16:25:48 [INFO] epitome_filter: Wrote 8960 kept records → updated.jsonl.gz
2026-06-24 16:25:48 [INFO] epitome_filter: ======================================================================
2026-06-24 16:25:48 [INFO] epitome_filter: Filter summary (>=10% coverage & >=80% identity)
2026-06-24 16:25:48 [INFO] epitome_filter: ----------------------------------------------------------------------
2026-06-24 16:25:48 [INFO] epitome_filter:   Input records        : 8965
2026-06-24 16:25:48 [INFO] epitome_filter:     with sequence      : 8965
2026-06-24 16:25:48 [INFO] epitome_filter:     without sequence   : 0
2026-06-24 16:25:48 [INFO] epitome_filter:   Aligned to a target  : 11
2026-06-24 16:25:48 [INFO] epitome_filter:   Removed              : 5
2026-06-24 16:25:48 [INFO] epitome_filter:   Kept                 : 8960
2026-06-24 16:25:48 [INFO] epitome_filter:     below threshold    : 6
2026-06-24 16:25:48 [INFO] epitome_filter:     no alignment       : 8954
2026-06-24 16:25:48 [INFO] epitome_filter:     no sequence        : 0
2026-06-24 16:25:48 [INFO] epitome_filter: ----------------------------------------------------------------------
2026-06-24 16:25:48 [INFO] epitome_filter: Removed records:
2026-06-24 16:25:48 [INFO] epitome_filter:   Lentivirus|wg|3825                  → NC_000001.11   cov=88.29%  id=99.46%
2026-06-24 16:25:48 [INFO] epitome_filter:   Lentivirus|wg|5653                  → NC_000010.11   cov=94.00%  id=99.61%
2026-06-24 16:25:48 [INFO] epitome_filter:   Lentivirus|wg|6651                  → NC_000006.12   cov=70.02%  id=99.92%
2026-06-24 16:25:48 [INFO] epitome_filter:   Lentivirus|wg|7194                  → NC_000019.10   cov=41.79%  id=99.97%
2026-06-24 16:25:48 [INFO] epitome_filter:   Lentivirus|wg|7734                  → NC_000011.10   cov=39.70%  id=99.97%
2026-06-24 16:25:48 [INFO] epitome_filter: ======================================================================

v2.0.4

Stray colon in tower.yml file caused failure on Seqera Cloud.

v2.0.3

What's Changed

• bug fix when references are supplied manually by @DOH-JDJ0303 in #26

Full Changelog: v2.0.2...v2.0.3

v2.0.2

What's Changed

• Fix indentation for assembly_tidy display entry by @DOH-JDJ0303 in #23
• Improvements to references and selection criteria by @DOH-JDJ0303 in #24

Full Changelog: v2.0.0...v2.0.2

v2.0.0

What's New

Major Changes

• Base functions have been rewritten in Python and now follow a standardized format: bin/vaper_*.py.
• The CDC IRMA assembler is no longer supported due to suspected issues with iterative reference refinement when multiple species or subtypes are present, which could lead to assembly errors.
• The fast reference selection mode has been removed. This method was not found to be faster or more accurate than the default accurate mode.
  • The former accurate mode is now referred to as standard. The accurate mode name will still work for backward compatibility.

New Modes and Behavior

• Added support for:
  • Consensus modes: standard, mixed
  • Reference selection modes: standard, sensitive, kitchen-sink
• Reference selection is now more sensitive and reproducible due to:
  • Deterministic processing at final selection steps
  • Improved reference refinement using Sourmash and DBSCAN
• Read alignment is now performed against all references simultaneously, improving efficiency and reducing spurious alignments, especially for closely related species.

Reference and Database Updates

• Introduced a new reference set containing all species targeted by the Illumina VSP v2.0 panel, plus hundreds of additional species (generated using EPITOME v2.1).
• Reference sets are now accepted in CSV or JSONL format (JSONL is standard).
• Reference selection supports include and exclude filtering via the samplesheet or command-line interface.
• Updated viral Sourmash database used for metagenomic analysis. This now requires git large file storage if cloning the repo to access the DB files. These files should still be staged automatically when the workflow is run.

Assembly and Output Improvements

• FASTQ files are no longer required to be gzip-compressed issue #6.
• Assemblies can optionally be output in a "tidy" format that:
  • Removes terminal N characters
  • Excludes mixed IUPAC ambiguity codes
  • Is suitable for GenBank submissions
• A detailed JSON summary is now generated in addition to the standard CSV summary.

Privacy and Compliance

• Reads can optionally be scrubbed of human sequences, facilitating submission to public repositories such as SRA.

Parameter Changes

• The default allele ratio threshold used by iVar has been changed from 0.6 to 0.
  • This reflects the true behavior of the parameter, despite current documentation.
  • See: consensus with ambiguities · Issue #51 · andersen-lab/ivar

New documentation page available at https://doh-jdj0303.github.io/vaper-docs/docs/v2.0/

v2.0.0-rc.1

Pre-release of v2.0.0.

Testing use of large file storage for Sourmash database files and its functionality with Nextflow staging.

v1.0.1

What's Changed

• Fix nextflow syntax error by @fanninpm in #21

New Contributors

• @fanninpm made their first contribution in #21

Full Changelog: v1.0...1.0.1

v1.0

VAPER v1.0 was validated using 100 samples from 17 different species (see table below), sequenced using the Illumina VSP v2.0 kit. All but one sample shared >99.6% identity with published sequences. The exception being the Monkeypox virus sample, which had higher error rates in the inverted terminal repeats. As a temporary solution, a helper script has been made to mask these repeat regions in Monkeypox genomes.

Species (subtypes)	n
Adenovirus	7
CoV-229E	4
CoV-HKU1	3
CoV-NL63	3
CoV-OC43	3
Enterovirus (D68)	1
Hepatitis A virus	1
Human Metapneumovirus	1
Influenza A (H3; H1; H1N1; H3N2)	10
Influenza B	5
Measles virus	11
Monkeypox virus (IIa)	1
Mumps virus	11
Parainfluenza (3 or 4; 1 or 2; 1; 4)	17
Respiratory syncytial virus (A; B)	4
SARS-CoV-2 (BA.4.1)	10
West Nile Virus	8

What's Changed

• Dev by @DOH-JDJ0303 in #1
• Norm ref by @DOH-JDJ0303 in #2
• added irma as option by @DOH-JDJ0303 in #3
• validation by @DOH-JDJ0303 in #5
• Irma sif by @DOH-JDJ0303 in #8
• Docker Hub -> ECR by @DOH-JDJ0303 in #9
• Dups patch by @DOH-JDJ0303 in #10
• Irma and refs by @DOH-JDJ0303 in #11
• account for samples where no sequences are classified by Sourmash by @DOH-JDJ0303 in #12
• touching up the final summary by @DOH-JDJ0303 in #13

Full Changelog: βeta...v1.0

beta

Version for beta testing.