Release notes:

PolySample context

Support has been introduced for submissions involving environmental sequence sets associated with multiple samples and taxonomic annotations. This context enables submission of a FASTA file containing sequences, a SAMPLE_TSV file mapping sequences to samples, and optionally a TAX_TSV file mapping sequences to taxa.

The following file group combinations are supported:

• 1 FASTA + 1 SAMPLE_TSV + 1 TAX_TSV
• 1 FASTA + 1 SAMPLE_TSV
• 1 TAX_TSV

New metadata fields have been added to support enriched environmental sequence submissions. These include:

• ANALYSIS_TYPE: Type of SEQUENCE_SET, currently supported value is ENVIRONMENTAL_SEQUENCE_SET. (Required when applicable.)
• ANALYSIS_PROTOCOL: Free-text protocol description.
• ANALYSIS_DATE: Date of analysis.
• TARGET LOCUS: Name of the targeted genetic locus.
• ANALYSIS CODE: Code identifying the analysis.
• ANALYSIS VERSION: Version number of the analysis.
• ORGANELLE: Organelle from which the sequences originated.
• FORWARD PRIMER NAME: Name of the forward primer.
• FORWARD PRIMER SEQUENCE: Sequence of the forward primer.
• REVERSE PRIMER NAME: Name of the reverse primer.
• REVERSE PRIMER SEQUENCE: Sequence of the reverse primer.
• ANALYSIS CENTER: Name of the analysis center.

These fields enhance the ability to capture detailed metadata required for multi-sample, sequence-based environmental analyses.

Release notes:

• Sequence context: Support has been introduced for the Environmental Sequence Set (ENVIRONMENTAL_SEQUENCE_SET) analysis type. This newly added analysis type enables users to submit a FASTA file containing sequences, along with a TSV file that maps each sequence to one or more samples while also specifying the frequency of each sequence within the associated samples.

• Sequence context: A new optional manifest field, ANALYSIS_TYPE, has been introduced. If a submission pertains to an ENVIRONMENTAL_SEQUENCE_SET analysis, the ANALYSIS_TYPE field is mandatory. The expected value for ANALYSIS_TYPE in this context is SEQUENCE_SET.

Release notes:

• Read context: added support for Illumina NovaSeq X Plus and DNBSEQ-T10×4RS instrument model.
• Genome context: block submissions with chromosome names specified as "contig" or "scaffold"
• Genome context: Enhancements to prevent overlapping gaps.

Release notes:

• genome context : AGP file support has been removed.
• All contexts : General security updates.

Release notes:

• All contexts : Only supports Java 17 and above.
• read context : uses latest tools for file processing.
• read context : bz2 compressed file format is now supported.
• read context : fixes how NOT_AUTCG characters are counted. previously it was per read and not per sample, which was incorrect.
• read context : other improvements and fixes.

Release notes:

• All contexts: Resolved an issue with the taxonomy API, which was causing the following error:
  Error while calling the url: http://wwwint.ebi.ac.uk/ena/taxonomy/rest/

Release notes:

• genome, transcriptome and sequence contexts: Support new qualifier /geo_loc_name as a replacement for the /country qualifier. Any /country qualifiers will be automatically converted to /geo_loc_name qualifier.

Release notes:

• genome and sequence contexts: Fixed the following error from being erroneously reported when the feature was 5' partial: Protein coding feature can be a single stop codon only if it has 3 bases and is 5' partial.
• genome and sequence contexts: Fixed a bug where partiality was erroneously rejected when using the order operator
• genome and sequence contexts: Fixed the following error from being erroneously reported: Anticodon amino acid abbreviation "..." is not matching with the sequence "..." using translation table "...".

Release notes:

• All contexts: support multiple submissions when using the JSON manifest. It is now possible to give an array of multiple JSON manifest objects in the manifest file instead of a single object.

Release notes:

• assembly, template, sequence context: support 'Czechia' country value in samples and sequence submissions.