Batching¶

Output from Oxford Nanopore Technologies products can be batched in various ways, depending on the software used to generate the files.

MinKNOW configuration¶

UI¶

The UI for MinKNOW allows configuring the batching for BAM and FASTQ based on "Time elapsed" and "Read count".

Default values¶

The default_writer.toml file in <minknow_install_dir>/conf/package/shared/default_writer.toml contains default batching parameters, and allows additional control on top of what the UI provides.

File format configuration locations¶

In the default_writer.toml config file batching for POD5 and .fast5 can be controlled:

File Type	Config Location
POD5	`[writer_configuration.read_pod5]`
.fast5	`[writer_configuration.read_fast5]`

Batching examples¶

The following examples can be used to replace existing batching options for a file format, to change how a file type is batched.

Batch based on read count¶

batch_duration = "0s"               # Time based batching disabled
batch_count = 4000                  # How many reads in each file

Batch into hourly files, or 500 million bases, whichever comes first¶

batch_duration = "3600s"            # Time based batch duration
bases_per_batch = 500_000_000       # Batch based on estimated base output

Batch into hourly files¶

batch_duration = "3600s"            # Time based batch duration
no_output_based_batching = {}       # Disable output based batching

Batch into 1 giga base files¶

bases_per_batch = 1_000_000_000     # Batch based on estimated base output