Basic Usage and Tests¶

The easiest way to test the pipeline is to run the tests, which will basecall, assemble and polish a small dataset that comes bundled with Katuali. The tests require suppy, pomoxis, canu, flye and medaka to be installed, and can be run with:

make test

The output is placed in nested directories under the folder test/. For example, if the test has run correctly a .bam alignment file will have been produced containing 25X coverage of reads basecalled with guppy aligning to and E.coli plasmid.

test/
  MinIonRun1/              # dataset name as defined in config.
    guppy/            # guppy basecaller with default options
      align/             # alignment of bases
        all_contigs/     # extraction of all_contigs in alignment
          25X/           # subsampling alignments
            sub_sample_25X_ecoli_SCS110_plasmid2.calls2ref.bam

Predefined Workflows¶

Katuali comes with a number of predefined workflows. To use these with your own data, start by creating a directory of reads (which could contain subdirectories of reads) within a run directory:

mkdir -p run1
cd run1
ln -s /path/to/fast5 reads  # create a softlink to the fast5 data
cd ..

Then make a copy of the katuali config into your working directory,

katuali_config my_config.yaml

and update this file to reflect your data:

DATA:
    'run1':
        'GENOME_SIZE': '4.0M'  # for canu/flye we need to specify genome size

There are two standard workflows available:

To perform basecalling, a quick assembly with miniasm, and consensus with racon and medaka it is sufficient to run:
```
katuali --configfile my_config.yaml all_fast_assm_polish
```
Alternatively to assemble with canu/flye (depending on ASSEMBLER option in my_config.yaml) run:
```
katuali --configfile my_config.yaml all_standard_assm_polish
```

The Custom pipelines section describes how to create a pipeline with any combination of basecallers, assemblers and polishers.