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# Quick start

Note that the Shasta executable has no dependencies and requires no installation or set up, except for setting its execute permission. See below for more information, including some small changes required for macOS and Windows.

## Linux

You can use the following commands to download the executable from the latest release and run an assembly:

    # Download the executable for the latest release.
    curl -O -L https://github.com/chanzuckerberg/shasta/releases/download/0.7.0/shasta-Linux-0.7.0

    # Grant necessary permissions.
    chmod ugo+x shasta-Linux-0.7.0

    # Run an assembly.
    ./shasta-Linux-0.7.0 --input input.fasta

You can specify multiple input FASTA files, if necessary. On a typical laptop, this will run in minutes for a bacterial genome. For a human size assembly, AWS instance type `x1.32xlarge` is recommended. It is usually available at a cost around $4/hour on the AWS spot market and should complete the human size assembly in a few hours, at coverage around 60x.

Assembly output will be created in a new directory named `ShastaRun`. Output includes the assembly in FASTA and GFA 1.0 formats in files:

- `ShastaRun/Assembly.fasta`
- `ShastaRun/Assembly.gfa`
- `ShastaRun/Assembly-BothStrands.gfa`

This will work on most current 64 bit Linux distributions. It was tested on at least the following Linux distributions for the `x86_64` architecture.

- Ubuntu 16.04 LTS
- Ubuntu 18.04 LTS
- Ubuntu 20.04 LTS

Note that the procedure above does not require root privilege, unless some non-default options are used when invoking the executable. Those non-default options are, however, necessary to achieve maximum performance.

## macOS

    # Download the executable for the latest release.
    curl -O -L https://github.com/chanzuckerberg/shasta/releases/download/0.7.0/shasta-macOS-0.7.0

    # Grant necessary permissions.
    chmod ugo+x shasta-macOS-0.7.0

    # Run an assembly.
    ./shasta-macOS-0.7.0 --input input.fasta

The macOS executable has been tested on macOS 10.15 (Catalina) and macOS 10.14 (Mojave).

## Windows

- Install Windows Subsystem for Linux (WSL).
- Working in a Linux shell created using WSL, follow the directions for Linux above.

## Quick test and demonstration

You can use the following commands to run a quick test and demonstration of the Shasta assembler:

    curl -O -L https://s3-us-west-2.amazonaws.com/lc2019/shasta/ecoli_test/r94_ec_rad2.181119.60x-10kb.fasta.gz
    gunzip r94_ec_rad2.181119.60x-10kb.fasta.gz
    /path/to/shasta_executable --input r94_ec_rad2.181119.60x-10kb.fasta

The first two commands download and decompress an input fasta file containing Oxford Nanopore reads for E. coli. The last command runs a Shasta assembly, which should complete in a few minutes on a laptop with at least 8 GB of memory. Assembly output will appear in a new directory `ShastaRun`. See in particular `ShastaRun/Assembly.fasta` and `ShastaRun/Assembly.gfa`.

## For more information

More detailed information on running an assembly is available here. A list of command line options can be found here.

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