smftools.informatics.basecalling

Functions

canoncall(model_dir, model, pod5_dir, ...[, ...])	Wrapper function for dorado canonical base calling.
modcall(model_dir, model, pod5_dir, ...[, ...])	Wrapper function for dorado modified base calling.

smftools.informatics.basecalling.canoncall(model_dir, model, pod5_dir, barcode_kit, bam, bam_suffix, barcode_both_ends=False, trim=False, device='auto', emit_moves=False)

Wrapper function for dorado canonical base calling.

Parameters:

• model_dir (str) -- a string representing the file path to the dorado basecalling model directory.

• model (str) -- a string representing the the dorado basecalling model.

• pod5_dir (str) -- a string representing the file path to the experiment directory containing the POD5 files.

• barcode_kit (str) -- A string reppresenting the barcoding kit used in the experiment. Needed for demultiplexing

• bam (str) -- File path to the BAM file to output.

• bam_suffix (str) -- The suffix to use for the BAM file.

• barcode_both_ends (bool) -- Whether to require a barcode detection on both ends for demultiplexing.

• trim (bool) -- Whether to trim barcodes, adapters, and primers from read ends.

• device (str) -- The device to use. 'auto' is default, which can detect device to use. Can also specify metal, cpu, cuda.

• emit_moves (bool) -- Whether to emit move tables (mv tag) for signal-to-base alignment.

Returns:

None

Outputs a BAM file holding the canonical base calls output by the dorado basecaller.

smftools.informatics.basecalling.modcall(model_dir, model, pod5_dir, barcode_kit, mod_list, bam, bam_suffix, barcode_both_ends=False, trim=False, device='auto', emit_moves=False)

Wrapper function for dorado modified base calling.

Parameters:

• model_dir (str) -- a string representing the file path to the dorado basecalling model directory.

• model (str) -- a string representing the the dorado basecalling model.

• pod5_dir (str) -- a string representing the file path to the experiment directory containing the POD5 files.

• barcode_kit (str) -- A string representing the barcoding kit used in the experiment.

• mod_list (list) -- A list of modification types to use in the analysis.

• bam (str) -- File path to the BAM file to output.

• bam_suffix (str) -- The suffix to use for the BAM file.

• barcode_both_ends (bool) -- Whether to require a barcode detection on both ends for demultiplexing.

• trim (bool) -- Whether to trim barcodes, adapters, and primers from read ends

• device (str) -- Device to use for basecalling. auto, metal, cpu, cuda.

• emit_moves (bool) -- Whether to emit move tables (mv tag) for signal-to-base alignment.

Returns:

None

Outputs a BAM file holding the modified base calls output by the dorado basecaller.