ncbi / ncbi/datasets

"Total" sequence length doesn't include organelles

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Description

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Describe the bug

Hello NCBI !

The assembly GCA_964199945.1 is reported as having a "Total Sequence Length" of 1,327,610,284 bp, but the the Fasta file actually contains 1,328,070,353 bp. The difference is exactly the MT and the plastid.

In https://www.ncbi.nlm.nih.gov/datasets/docs/v2/reference-docs/command-line/dataformat/tsv/dataformat_tsv_genome/:

assmstats-total-sequence-len Assembly Stats Total Sequence Length

To Reproduce

$ datasets summary genome accession GCA_964199945.1 --as-json-lines | dataformat tsv genome --fields assmstats-total-sequence-len --elide-header
1327610284

Expected behavior

I would expect the "total" sequence length to include everything. I would otherwise call it the length of "nuclear" genome only.

Best regards,
Matthieu

Contributor guide

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First steps

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Research direction

Start by running the datasets summary genome accession GCA_964199945.1 --as-json-lines | dataformat tsv genome --fields assmstats-total-sequence-len --elide-header command shown in the issue and compare its result with the FASTA contents. Trace how the total is calculated for this assembly, including its MT and plastid sequences. Done when the reported total matches the complete FASTA sequence length.

Written by the indexing model from the issue text.

Assessment

Domain
cli, data
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Clearly specified
Newbie friendliness
40/100

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