# polypolish 0.5.0


## Polypolish

Polypolish is a tool for polishing genome assemblies with short reads. Unlike
other tools in this category, Polypolish uses SAM files where each read has
been aligned to _all_ possible locations (not just a single best location).
This allows it to repair errors in repeat regions that other alignment-based
polishers cannot fix.

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

Location and version:

```console
$ which polypolish
/local/cluster/polypolish/polypolish
$ polypolish --version
Polypolish v0.5.0
```

help message:

```console
$ polypolish --help
  _____        _                       _  _       _
 |  __ \      | |                     | |(_)     | |
 | |__) |___  | | _   _  _ __    ___  | | _  ___ | |__
 |  ___// _ \ | || | | || '_ \  / _ \ | || |/ __|| '_ \
 | |   | (_) || || |_| || |_) || (_) || || |\__ \| | | |
 |_|    \___/ |_| \__, || .__/  \___/ |_||_||___/|_| |_|
                   __/ || |
                  |___/ |_|

Polypolish v0.5.0

short-read polishing of long-read assemblies
github.com/rrwick/Polypolish

USAGE:
    polypolish [OPTIONS] <ASSEMBLY> <SAM>...

ARGS:
    <ASSEMBLY>    Assembly to polish (one file in FASTA format)
    <SAM>...      Short read alignments (one or more files in SAM
                  format)

OPTIONS:
    -d, --min_depth <MIN_DEPTH>
            A base must occur at least this many times in the pileup to
            be considered valid [default: 5]

        --debug <DEBUG>
            Optional file to store per-base information for debugging
            purposes

    -h, --help
            Print help information

    -i, --fraction_invalid <FRACTION_INVALID>
            A base must make up less than this fraction of the read depth
            to be considered invalid [default: 0.2]

    -m, --max_errors <MAX_ERRORS>
            Ignore alignments with more than this many mismatches and
            indels [default: 10]

    -v, --fraction_valid <FRACTION_VALID>
            A base must make up at least this fraction of the read depth
            to be considered valid [default: 0.5]

    -V, --version
            Print version information
```

software ref: <https://github.com/rrwick/Polypolish>  
software ref: <https://github.com/rrwick/Polypolish/wiki>  
research ref: <https://doi.org/10.1371/journal.pcbi.1009802>