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Quick start

Selecting a machine

The Shasta executable has no dependencies and requires no installation or set up. It will run on almost any 64-bit Linux machine, regardless of distribution.

Downloading the executable

You can download the executable for the latest release from the Shasta releases page. The Linux executable for release X.Y.Z is named shasta-Linux-X.Y.Z. For example, the current release at the time of writing is 0.14.0 and the executable is named shasta-Linux-0.14.0.

You can also download the executable from the command line, for example: 

wget https://github.com/paoloshasta/shasta/releases/download/0.14.0/shasta-Linux-0.14.0

Setting execute permission

You have to set the execute permission bit before you can run the executable. This can be done for example as follows (replace X.Y.Z consistently with the release you donwloaded): 

chmod ugo+x shasta-Linux-X.Y.Z

Downloading input reads for a test assembly

You can download from here a fasta file that can be used as input for a test assembly. This test covers a 2 Mb region of chromosome 1 for the HG002 human genome and was extracted from the error corrected dataset released by Oxford Nanopore (ONT) in May 2024.

Shasta does not accept compressed input files, so you must decompress the fasta.gz file before using it as input to Shasta: 

gunzip -d LC2024_HERRO_CORRECTED_chr1_34-36.fasta.gz

Running the test assembly

Now you are ready to run the test assembly: 

./shasta-Linux-0.14.0 --config Nanopore-r10.4.1_e8.2-400bps_sup-Herro-Jan2025 --input LC2024_HERRO_CORRECTED_chr1_34-36.fasta
This will create a directory ShastaRun containing, among other files, the assembly output in fasta and gfa formats, Assembly.fasta and Assembly.gfa.

The --config option specifies an "assembly configuration" that selects assembly options appropriate to a specific type of reads. The assembly configuration used above is optimized for Ultra-Long (UL), error corrected reads from the ONT May 2024 data release. If you have a different type of reads, see this page for a summary of other available assembly configurations.

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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