We will be using albacore 1.1.1, which is available to download from the ONT community.

If we run without any options, then we get usage instructions:

This produces:

usage: [-h] [-l] [-v] -i INPUT -t WORKER_THREADS -s
                                SAVE_PATH [-f FLOWCELL] [-k KIT] [--barcoding]
                                [-c CONFIG] [-d DATA_PATH] [-b] [-r]
                                [-n FILES_PER_BATCH_FOLDER] [-o OUTPUT_FORMAT]
                                [-q READS_PER_FASTQ_BATCH] error: the following arguments are required: -i/--input, -t/--worker_threads, -s/--save_path

And if we run with -h, we get a bit more help ;-) -h


usage: [-h] [-l] [-v] -i INPUT -t WORKER_THREADS -s
                                SAVE_PATH [-f FLOWCELL] [-k KIT] [--barcoding]
                                [-c CONFIG] [-d DATA_PATH] [-b] [-r]
                                [-n FILES_PER_BATCH_FOLDER] [-o OUTPUT_FORMAT]
                                [-q READS_PER_FASTQ_BATCH]

ONT Albacore Sequencing Pipeline Software

optional arguments:
  -h, --help            show this help message and exit
  -l, --list_workflows  List standard flowcell / kit combinations.
  -v, --version         Print the software version.
  -i INPUT, --input INPUT
                        Folder containing read fast5 files (if not present,
                        will expect file names on stdin).
  -t WORKER_THREADS, --worker_threads WORKER_THREADS
                        Number of worker threads to use.
  -s SAVE_PATH, --save_path SAVE_PATH
                        Path to save output.
  -f FLOWCELL, --flowcell FLOWCELL
                        Flowcell used during the sequencing run.
  -k KIT, --kit KIT     Kit used during the sequencing run.
  --barcoding           Search for barcodes to demultiplex sequencing data.
  -c CONFIG, --config CONFIG
                        Optional configuration file to use.
  -d DATA_PATH, --data_path DATA_PATH
                        Optional path to model files.
  -b, --debug           Output additional debug information to the log.
  -r, --recursive       Recurse through subfolders for input data files.
  -n FILES_PER_BATCH_FOLDER, --files_per_batch_folder FILES_PER_BATCH_FOLDER
                        Maximum number of files in each batch subfolder. Set
                        to 0 to disable batch subfolders.
  -o OUTPUT_FORMAT, --output_format OUTPUT_FORMAT
                        desired output format, can be fastq,fast5 or only one
                        of these.
  -q READS_PER_FASTQ_BATCH, --reads_per_fastq_batch READS_PER_FASTQ_BATCH
                        number of reads per FastQ batch file. Set to 0 to
                        receive one reads per file and file names which
                        include the read ID.

It’s really important to know the workflow you used in sequencing to be able to basecall. We can list possible options: -l

This produces a list of available configs:

Parsing config files in /opt/albacore.
Available flowcell + kit combinations are:
flowcell    kit         barcoding  config file
FLO-MIN106  SQK-LSK108             r94_450bps_linear.cfg
FLO-MIN106  SQK-LSK208             r94_250bps_2d.cfg
FLO-MIN106  SQK-LWB001  included   r94_450bps_linear.cfg
FLO-MIN106  SQK-LWP001             r94_450bps_linear.cfg
FLO-MIN106  SQK-NSK007             r94_250bps_nsk007_2d.cfg
FLO-MIN106  SQK-RAB201  included   r94_450bps_linear.cfg
FLO-MIN106  SQK-RAD002             r94_450bps_linear.cfg
FLO-MIN106  SQK-RAS201             r94_450bps_linear.cfg
FLO-MIN106  SQK-RBK001  included   r94_450bps_linear.cfg
FLO-MIN106  SQK-RLB001  included   r94_450bps_linear.cfg
FLO-MIN106  SQK-RLI001             r94_450bps_linear.cfg
FLO-MIN106  SQK-RNA001             r94_70bps_rna_linear.cfg
FLO-MIN106  VSK-VBK001             r94_450bps_linear.cfg
FLO-MIN107  SQK-LSK108             r95_450bps_linear.cfg
FLO-MIN107  SQK-LSK308             r95_450bps_linear.cfg
FLO-MIN107  SQK-LWB001  included   r95_450bps_linear.cfg
FLO-MIN107  SQK-LWP001             r95_450bps_linear.cfg
FLO-MIN107  SQK-RAB201  included   r95_450bps_linear.cfg
FLO-MIN107  SQK-RAD002             r95_450bps_linear.cfg
FLO-MIN107  SQK-RAS201             r95_450bps_linear.cfg
FLO-MIN107  SQK-RBK001  included   r95_450bps_linear.cfg
FLO-MIN107  SQK-RLB001  included   r95_450bps_linear.cfg
FLO-MIN107  SQK-RLI001             r95_450bps_linear.cfg
FLO-MIN107  VSK-VBK001             r95_450bps_linear.cfg

Finally, as base-calling is such a very compute intensive operation, we should only do this on a subset of files. A command might look like this: -i /vol/raw_fast5/ \
                         -r \
                         -t 4 \
                         -s basecalled_dir \
                         -o fastq,fast5 \
                         -c r94_450bps_linear.cfg \

In turn these options mean

If you run this, please only do this on a small subset of files!