Assembling genomes on Pawsey using Autocycler
Autocycler is undoubtedly the best assembler, especially for Oxford Nanopore sequencing of bacterial genomes. You often get complete circular genomes.
We are going to use autocycler on Pawsey to assembled a genome!
We are really following the instructions that Ryan Wick provided, and they are excellent
Before you begin, please install conda and create an autocycler environment.
Once you have installed those commands, please run this command to update plassembler:
mamba activate /scratch/$PAWSEY_PROJECT/$USER/software/miniconda3/autocycler
plassembler download -d "$CONDA_PREFIX"/plassembler_db
Note, we also have an autocycler installer slurm script that does everything!
To run autocycler you need:
- A fastq file with your sequences that you want to assemble.
- The autocycler run assmebly slurm script
You should be able to run this with the command:
sbatch autocycler_run.slurm reads.fastq assembly
The assembly process will take a while, and you can see the outputs in the temporary directory. Check the error log for the location of those files.
Once complete, your output should be in assembly