29th INSDC meeting report: May 16-18 2016, Hinxton, UK

2016

29th INSDC meeting report: May 16-18 2016, Hinxton, UK

International Nucleotide Sequence Database Collaboration (INSDC), consisted of DDBJ, EBI and NCBI, hold the international meeting every year.
In 2016, the meeting was held at EBI, 16-18 May, to discuss practical matters to maintain and update nucleotide sequence data archives; DDBJ, ENA, GenBank, Sequence Read Archive (SRA) and Trace Archive.
The outcomes of the meeting are summarized below.

The Items; Discussed and To Be Studied

NGS Quality Scores

Currently, 70-80% of SRA storage is for quality scores, however, most of bioinformatic tools do not use them.
For the long haul, we, INSDC, prefer to round down (i.e. binning or 8 binning) or to throw away quality scores for inhibition of SRA data increasing.
But, the needs for quality scores might be different depending on research areas.
We would like to discuss about how to accept future NGS data with major research communities, broadly.

SRA Objects VS BioProject/BioSample

The relationships between SRA study object and BioProject and between SRA sample object and BioSample were considered.

Introduction of Targeted Locus Study (TLS) data

GenBank has started to accept submissions of bulk sequence data including 16S rRNA or some other targeted loci to be clustered into operational taxonomic unit as TLS data with four-letter prefix accession numbers like as WGS.

INSDC Data Status

We discussed practical procedures about data exchange among databanks, especially, INSDC status for bulk data like WGS and TSA and also for SRA, BioProject and BioSample records.

Assembly (Genome Collection)

To enhance the collaboration with Assembly since 2012, we discussed some practical issues.

Forthcoming Changes in The DDBJ/ENA/GenBank Feature Table: Definition

The following items were proposed to be applied for Feature Table Definition from the next revision or later.

For rep_origin feature, the /function qualifier will be available.

Expansion of definition of regulatory feature to describe regulation of replication.

Addition of some controlled vocabularies for /regulatory_class qualifier.

Addition of one feature key and one qualifier key to clarify current descriptions of miscellaneous features.

• propeptide feature to describe intermediate of peptide maturation
• /recombination_class qualifier for misc_recomb feature