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# SamSifter

SamSifter helps you create filter workflows for next-generation sequencing data. It is primarily used to process SAM files generated by MALT prior to metagenomic analysis in MEGAN.

## Quick Start

### Installing SamSifter

Installing or updating SamSifter is easy once you have a working Python3 environment with `PyQt4`, `matplotlib`, `numpy` and `pandas`. See the Detailed Installation Instructions for help on installing these required packages.

Download and install the current SamSifter package on your system by executing the following command as administrator:

    pip3 install SamSifter

Previous versions will be uninstalled automatically. The installation can be tested with

    samsifter --help

If everything went fine you should see the following help text:

    usage: samsifter [-h] [-v] [-d]

    SamSifter helps you create filter workflows for next-generation sequencing
    data. It is primarily used to process SAM files generated by MALT prior to
    metagenomic analysis in MEGAN.

    optional arguments:
      -h, --help     show this help message and exit
      -v, --verbose  print additional information to stderr
      -d, --debug    show debug options in menu

Starting the program without any arguments will display the GUI and let you edit your first workflow.

### First Steps

To start working add filters to the empty workflow. You can add filters by doubleclicking available entries in the righthand dock or by selecting an entry from the menu [Edit > Add Filter...]. Similarly, you can doubleclick filters in the workflow to edit their settings and parameters. The lefthand toolbar is used to move and delete filter steps. For more information on editing workflows see Creating and Editing Workflows.

You can save your workflow to a file, execute it right now by clicking the [Run] button and even export it to a Bash script to run it on another workstation. Any errors and messages will be reported to you in the message dock at the bottom of the window.

Feel free to re-arrange these docks to make yourself comfortable - SamSifter will remember your settings. Accidentally closed docks can always be re-opened from the menu [View].

### Uninstalling SamSifter

To get rid of SamSifter simply execute the following command as administrator:

    pip3 uninstall SamSifter

The Python utility `pip3` will list all currently installed available versions for selective removal. Proceed similarly with any required packages (e.g. `matplotlib`) if you don’t need them anymore.

## Manual and Help

- SamSifter Help
  - Manual
  - Frequently Asked Questions
  - Known Bugs

## API documentation

Developers interested in extending the program’s functionalities may find the following pages useful:

- SamSifter API documentation
  - pmdtools package
  - samsifter package

## Indices and tables

- Index
- Module Index
- Search Page

### Navigation

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