Chronostrain Manuscript: BBS Analysis Database and Output

This upload contains files pertaining to the BabyBiome analysis as it appears in the ChronoStrain publication (2025 Kim et al.). Specifically, this repository contains the following files related to the analysis of the BabyBiome Study (2019 Shao et al.) on those samples with cultured E. faecalis isolates.

Instructions: To use these files, please download all files and extract each archive into the same folder. For instance: tar -xvzf ELMC_*.tar.gz -C target_dir. These unpacked files can then be used by the jupyter notebook infant-nt/notebooks/timeseries_plots.ipynb found in the chronostrain paper repository. Please refer to the README file (infant-nt/README.md) for step-by-step instrucitons.

1. Database files for ChronoStrain (99.8% clustering) -- normal and mutated  -- [ELMC_chronostrain_db*]
2. Database files for mGEMS (tuned to match ChronoStrain's ELMC isolate granularity) -- normal and mutated  -- [ELMC_mgems_db*]
3. fastMLST annotations for genomes (newly added in v2) -- [ELMC_fastmlst.tar.gz -- newly added in v2]
4. Outputs for all infants using both methods (five analyses total) -- [ELMC_output.tar.gz.part* + ELMC_chronostrain_99_99pct.tar.gz]
   
   • chronostrain
   • chronostrain w/ fine-grained database (chronostrain_99_99pct.tar.gz -- newly added in v2)
   • chronostrain w/ mutation
   • mgems (original nat.comm. index)
   • mgems (chronostrain re-tuned)
   • mgems (re-tuned and w/ mutation)
5. TSV tables containing outputs (generated using the notebook examples/infant-nt/notebooks/inference_comparison.ipynb) --- [infant_analysis_tables.zip]
6. A TSV table listing the non-Efaecalis genomes used to construct ChronoStrain's database -- [Enterococcaceae_index.tsv]
   • Note: this index includes RefSeq E.faecalis genome, which were excluded from the database construction. For analysis, the only E.faecalis genomes included were the ~2000 European E.faecalis isolates (2021 Pontinen et al.) and the ~350 ELMC infant isolates -- those isolates are not listed on this TSV file. Refer to the notebook "examples/infant-nt/notebooks/database_efaecalis_elmc.ipynb" to see how this is used.

[Note 1: the output files have been split into ~500MB parts using the "split" utility in linux. To re-join them, use the command cat ELMC_output.tar.gz.part* > ELMC_output.tar.gz]

[Note 2: We formerly called this dataset "Early life microbiota cohort (ELMC)" on an earlier version of our paper, and thus the filenames have an "ELMC_" prefix for legacy reasons.]