Very quick start

This page shows how to run Autocycler with the absolute minimum of setup and explanation.

1. Installation

You'll need to install Autocycler and several long-read assemblers. You can use this environment file to put everything in one conda environment.

2. Run Autocycler

You can use this Bash script to run the full Autocycler pipeline in one command:

autocycler_full.sh reads.fastq.gz 16 4

Where reads.fastq.gz is your input long-read file, 16 is the number of threads to use and 4 is the number of parallel jobs (for running multiple assemblers at once).

3. Get your assembly

When the script is complete, your final assembly will be here: autocycler_out/consensus_assembly.fasta.