From 6685c3c07cccdc371b37bf308984cd4d94589221 Mon Sep 17 00:00:00 2001 From: Tom Stanton Date: Wed, 22 Jan 2025 16:37:43 +1100 Subject: [PATCH] Create README.md --- .../Auto-Autocycler_by_Tom_Stanton/README.md | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 pipelines/Auto-Autocycler_by_Tom_Stanton/README.md diff --git a/pipelines/Auto-Autocycler_by_Tom_Stanton/README.md b/pipelines/Auto-Autocycler_by_Tom_Stanton/README.md new file mode 100644 index 0000000..37901b1 --- /dev/null +++ b/pipelines/Auto-Autocycler_by_Tom_Stanton/README.md @@ -0,0 +1,33 @@ +# autoautocycler + +`autoautocycler` is a simple shell wrapper around [Autocycler](https://github.com/rrwick/Autocycler.git) for running all steps on multiple assemblies with a single command. + +## Installation +No installation required! Just make sure [Autocycler](https://github.com/rrwick/Autocycler.git) is installed and make the script excecutable with +`chmod +x autoautocycler.sh`. + +## Usage +Running `./autoautocycler.sh` with `-h`/`--help` will print all options: + +```sh +Usage: autoautocycler [ ...] [options] + Long reads to assemble in fastq(.gz) format + -o, --out Output directory (default: .) + -t, --threads #threads to use (default: all available) + -c, --count #subsampled read sets to output (default: 4) + -k, --kmer K-mer size for De Bruijn graph (default: 51) + -s, --size Genome size (default: AUTO) + -a, --assemblers Assemblers to use (default: all available) + Possible assemblers: canu flye lja metamdbg miniasm necat nextdenovo raven redbean + Note: this argument MUST BE WRAPPED in quotes +``` + +E.g. for making assemblies with flye, miniasm and raven, just run: +```sh +./autoautocycler.sh -o autocycler -c 2 -s 5500000 -a "flye miniasm raven" reads/*.fastq.gz +``` +Here I've set the subsampling count to 2 and set the genome size to 5500000 to skip the automatic genome size calculation with raven. + +## Bug reporting +Bugs can be reported using the [Autocycler issues page](https://github.com/rrwick/Autocycler/issues) on GitHub, +just make sure you tag me with @tomdstanton.