# trycycler 0.5.3


## Trycycler

Trycycler is a tool for generating consensus long-read assemblies for
bacterial genomes. I.e. if you have multiple long-read assemblies for the same
isolate, Trycycler can combine them into a single assembly that is better than
any of your inputs.

For installation instructions, usage, deeper explanations and more, head over
to the [Trycycler wiki](https://github.com/rrwick/Trycycler/wiki)!

## Using in SGE\_Batch

Make sure you are in bash, and generate a shell script with your commands
that you want to submit over SGE. Add the `source
/local/cluster/trycycler/activate.sh` line before your commands to access
the programs over SGE.

To activate:

```console
bash
source /local/cluster/trycycler/activate.sh
```

Location and version:

```console
$ which trycycler
/local/cluster/trycycler/bin/trycycler
$ trycycler --version
Trycycler v0.5.3
```

help message:

```console
$ trycycler --help
usage: trycycler [-h] [--version]
                 {subsample,cluster,dotplot,reconcile,msa,partition,consensus}
                 ...

 _______                               _
|__   __|                             | |
   | | _ __  _   _   ___  _   _   ___ | |  ___  _ __
   | || '__|| | | | / __|| | | | / __|| | / _ \| '__|
   | || |   | |_| || (__ | |_| || (__ | ||  __/| |
   |_||_|    \__, | \___| \__, | \___||_| \___||_|
              __/ |        __/ |
             |___/        |___/

Trycycler: a consensus long-read assembly tool

Commands:
  {subsample,cluster,dotplot,reconcile,msa,partition,consensus}
                        subsample: subsample a long-read set
                        cluster:   cluster contigs by similarity
                        dotplot:   draw pairwise dotplots for a cluster
                        reconcile: reconcile contig sequences
                        msa:       multiple sequence alignment
                        partition: partition reads by cluster
                        consensus: derive a consensus sequence

Help:
  -h, --help            Show this help message and exit
  --version             Show program's version number and exit
```

software ref: <https://github.com/rrwick/Trycycler>  
software ref: <https://github.com/rrwick/Trycycler/wiki>  
research ref: <https://doi.org/10.1186/s13059-021-02483-z>