API Reference¶

BASALT is primarily a command-line tool. This section provides reference documentation for the core Python modules.

Core Modules¶

Module	Description
`BASALT.py`	CLI argument parsing and workflow dispatch
`BASALT_main_d.py`	Main pipeline orchestration (CheckM2 branch)
`model.py`	MLP neural network architecture for contamination detection
`ensemble.py`	Model ensemble inference for S5 outlier removal
`utils.py`	Utility functions for training and evaluation
`my_dataset.py`	PyTorch Dataset for loading contig features

Module	Pipeline Stage
`S1_Autobinners_2qc_11152023.py`	S1: Multi-binner execution and initial QC
`S1e_extra_binners.py`	S1e: Extra binner integration (MetaBinner, VAMB, LorBin)
`S2_BinsAbundance_PE_connections_*.py`	S2: Abundance profiling and PE connectivity
`S3_Bins_comparator_within_group_*.py`	S3: Within-assembly bin comparison
`S4_Multiple_Assembly_Comparitor_*.py`	S4: Cross-assembly dereplication
`S5_Outlier_remover_DL_*.py`	S5: DL-based contamination removal
`S6_retrieve_contigs_from_PE_contigs_*.py`	S6: PE-based contig retrieval
`S7_Contigs_retrieve_within_group_*.py`	S7: Within-group contig retrieval
`S7lr_finding_sr_contigs_basing_lr_and_polishing_*.py`	S7lr: Long-read contig retrieval + polishing
`S8_OLC_new_*.py`	S8: Overlap-Layout-Consensus
`S9_Reassembly_*.py`	S9: Short-read reassembly (SPAdes)
`S9p_Hybrid_Reassembly_*.py`	S9p: Hybrid reassembly (Unicycler)
`S10_OLC_new_*.py`	S10: Final OLC refinement

Module	Description
`Data_feeding.py`	External binset import and coverage recalculation
`gen_kmer.py`	k-mer frequency computation for MetaBinner
`Cleanup.py`	Intermediate file cleanup
`Final_drep.py`	Final dereplication of binsets
`Cytoscapeviz.pl`	Cytoscape connection visualization (Perl)
`calc.kmerfreq.pl`	k-mer frequency calculation (Perl)
`jgi_summarize_bam_contig_depths`	BAM depth summary (JGI tool)