isoSeQL

Docker container for isoSeQL, a database tool for comparing long-read isoforms across multiple datasets analyzed with SQANTI3.

Upstream

• Upstream repository: https://github.com/christine-liu/isoSeQL
• Upstream version packaged here: v1.0.0

Citation

Liu CS, Chun JC. isoSeQL: comparing long-read isoforms across multiple datasets. Bioinformatics. 2026;42(1):btaf680. https://doi.org/10.1093/bioinformatics/btaf680

Container image

docker pull picotainers/isoseql:latest

Included commands

• isoseql-run
• isoseql-query
• isoseql-scquery

The default container entrypoint is isoseql-query --help.

Usage

Show the built-in query help:

docker run --rm picotainers/isoseql:latest --help

Build an example database from the upstream bundled example data:

docker run --rm -v "$PWD:/work" --entrypoint /bin/bash picotainers/isoseql:latest -lc '
  isoseql-run \
    --classif /opt/isoseql/example/example_data/NA18989_filtered_classification.txt \
    --genePred /opt/isoseql/example/example_data/NA18989.genePred \
    --sampleConfig /opt/isoseql/example/example_data/NA18989_samp.config \
    --expConfig /opt/isoseql/example/example_data/NA18989_exp.config \
    --db /work/example.db
'

Query experiment metadata from that database:

docker run --rm -v "$PWD:/work" --entrypoint /bin/bash picotainers/isoseql:latest -lc '
  isoseql-query expInfo --db /work/example.db --out /work/example_expInfo.txt
  cat /work/example_expInfo.txt
'

Runtime notes

• This image follows the upstream conda-oriented dependency model using micromamba for reliability.
• gffread is included for workflows that pass --gff to isoseql-run.
• The image includes the upstream example dataset under /opt/isoseql/example/.