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apollo

DOI

Quick links


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                                        0.1
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                            Aine O'Toole & Tom Little           
                                Edinburgh University

Requirements

apollo runs on MacOS and Linux. The conda environment recipe may not build on Windows (and is not supported) but apollo can be run using the Windows subsystem for Linux.

  1. Some version of conda, we use Miniconda3. Can be downloaded from here
  2. Basecalled nanopore fastq files

Installation

  1. git clone https://github.com/WildANimalClocks/apollo.git and cd apollo
  2. conda env create -f environment.yml
  3. conda activate apollo
  4. python setup.py install

Note: we recommend using apollo in the conda environment specified in the environment.yml file as per the instructions above. If you can't use conda for some reason, dependency details can be found in the environment.yml file.

Check the install worked

Type (in the apollo environment):

apollo -v

and you should see the version number of apollo printed

Updating apollo

Note: Even if you have previously installed apollo, as it is being worked on intensively, we recommend you check for updates before running.

To update:

  1. conda activate apollo
  2. git pull
    pulls the latest changes from github
  3. python setup.py install
    re-installs apollo
  4. conda env update -f environment.yml
    updates the conda environment

Troubleshooting update

  • If you have previously installed apollo using pip, you will need to update apollo in the same way (pip install .)
  • Try pip uninstall apollo and then re-install with python setup.py install

Input options

-c / --config

apollo can accept a config file in yaml (or yml) format. This is a standard config format that describes the analysis you want to run.

You can provide any of the command line arguments via this config file, for instance pass the species or read_path in through via the configuation file.

Using this input option will allow the user to run similar reports again and again, without having to specify all arguments via the command line.

Note, if the same option is specified in the config file and as a command line argument, the command line argument will overwrite the config file option.

apollo -c config.yaml

If no config file is specified via the command line, apollo will look for a file called config.yaml in the current working directory.

Example config.yaml file:

demultiplex: True
outdir: config_test

read_path: path/to/mus_basecalled
path_to_guppy: ~/ont-guppy-cpu/bin/guppy_barcoder

barcode_kit: native

species: mus

threads: 4

apollo config file notes

  • Config keys are insensitive to '-' and '_' differences. Example: --read-path can be added to the config.yaml file as read_path or read-path
  • All command line options are available to be input in the config file

Command line args

See the help menu of apollo for full command line options, all are configurable in the config.yaml file too.

Usage

If you have a config.yaml file in the same directory that you’re in, all you need to write is:

apollo

and it’ll detect the config file and run the software with all the settings given in the config file.

If the config file isn’t in the same directory as you are (or is called soemthing different) you can say:

apollo -c path/to/config.yaml

if you don’t have a config file and just want to run the tool on the command line you can input:

apollo --read-path path/to/fastq/reads \
         --demultiplex \
         --species mus \
         -t 3 \
         --path-to-guppy path/to/guppy_barcoder

To run demultiplexing like above, you have either have guppy installed in your path or give apollo the path to the binary file you download from the ont community (guppy can’t be installed with the conda command because of ont rules).

If your reads are already demultiplexed (say in MinKNOW) you can input:

apollo --read-path path/to/demuxed/reads \
          --species mus \
          -t 3

Full usage:

usage: apollo -i <path/to/reads> [options]
       apollo -c <config.yaml>

optional arguments:
  -h, --help            show this help message and exit

input output options:
  -c CONFIGFILE, --configfile CONFIGFILE
                        Config file with apollo run settings
  -i READ_PATH, --read-path READ_PATH
                        Path to the directory containing fastq files
  -o OUTPUT_PREFIX, --output-prefix OUTPUT_PREFIX
                        Output prefix. Default: apollo_<species>_<date>
  --outdir OUTDIR       Output directory. Default: current working directory
  --tempdir TEMPDIR     Specify where you want the temp stuff to go. Default:
                        $TMPDIR

barcode options:
  -b BARCODES_CSV, --barcodes-csv BARCODES_CSV
                        CSV file describing which barcodes were used on which
                        sample
  -k BARCODE_KIT, --barcode-kit BARCODE_KIT
                        Indicates which barcode kit was used. Default: native.
                        Options: native, rapid, pcr, all

demultiplexing options:
  --demultiplex         Indicates that your reads have not been demultiplexed
                        and will run guppy demultiplex on your provided read
                        directory
  --path-to-guppy PATH_TO_GUPPY
                        Path to guppy_barcoder executable

run options:
  -s SPECIES, --species SPECIES
                        Indicate which species is being sequenced. Options:
                        mus, apodemus
  -r, --report          Generate markdown report of estimated age

misc options:
  -t THREADS, --threads THREADS
                        Number of threads
  --no-temp             Output all intermediate files, for dev purposes.
  --verbose             Print lots of stuff to screen
  -v, --version         show program's version number and exit

Output options

Description of output apollo directory

-o / --output-prefix and --outdir

An output prefix can be specified with -o /--output-prefix. If no output directory is specified, by default the directory will be a timstamped directory beginning with the output_prefix and the report files will be called output_prefix.md (Default: apollo) The output directory can be specified with --outdir, which overwrites the --output_prefix directory name. See example in the figure below: