Informatics: inform

Informatics module diagram

Processes raw sequencing data to load an adata object.

smftools.informatics.bam_functions
smftools.informatics.basecalling
smftools.informatics.bed_functions
smftools.informatics.binarize_converted_base_identities
smftools.informatics.complement_base_list
smftools.informatics.converted_BAM_to_adata(...)	Convert converted BAM files into an AnnData object with integer sequence encoding.
smftools.informatics.fasta_functions
smftools.informatics.fastq_export	Write per-barcode FASTQ files of reads directly from the raw ragged store.
smftools.informatics.h5ad_functions
smftools.informatics.modkit_extract_to_adata(...)	Convert modkit extract TSVs and BAMs into an AnnData object.
smftools.informatics.modkit_functions
smftools.informatics.ohe
smftools.informatics.partition_read	Assemble a concrete AnnData selection through the thin molecule spine.
smftools.informatics.partition_store	Zarr partition + thin molecule-index spine + partition catalog helpers.
smftools.informatics.pod5_functions
smftools.informatics.ragged_store	Read-relative molecule storage and reference-grid materialization.
smftools.informatics.raw_store	Write the ragged source-of-truth store and its thin molecule spine.
smftools.informatics.reference_identity	Canonical, name-independent reference identity via sequence hashing.
smftools.informatics.run_multiqc(input_dir, ...)	Run MultiQC on a directory and save the report to the output directory.
smftools.informatics.sequence_encoding
smftools.informatics.sidecar_manifest
smftools.informatics.signal_features	Per-base nanopore current features from the dorado move table.
smftools.informatics.storage_planner	Per-reference storage planning for locus and genome analyses.

The ragged_store/raw_store/partition_read/partition_store modules implement the v2.x partitioned storage architecture: a read-relative ragged parquet source of truth, a thin molecule-index spine.h5ad, and on-demand dense-slice materialization. fastq_export and sequence_encoding build on the ragged store to reconstruct literal read sequence/quality for FASTQ export.

Diagram of final steps of Direct SMF workflow

Diagram of final steps of Conversion SMF workflow