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pipelines/Auto-Autocycler_by_Tom_Stanton/README.md

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+# 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 <reads> [<reads> ...] [options]
+  <reads>            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.