Assemble a Genome
Create a new project named test_assembly
in the miga-data
directory:
Add your data set to the MiGA project. In doing this, turn off mytaxa scan and distances, as in the command below. MyTaxa is not installed in this version of MiGA, and because this project contains only one genome we cannot calculate distances. Here the -i flag specifies that the dataset being uploaded consists of trimmed reads.
For the input flag (-i), supported inputs include:
raw_reads_single: Single raw reads in a single FastQ file
raw_reads_paired: Paired raw reads in two FastQ files
trimmed_reads_single: Single trimmed reads in a single FastA file
trimmed_reads_paired: Paired trimmed reads in two FastA files
trimmed_reads_interleaved: Paired trimmed reads in a single FastA file
assembly: Assembled contigs or scaffolds in FastA format
Launch the daemon to start MiGA processing your data:
The shutdown-when-done
argument automatically stops the daemon when processing is finished.
After the job starts, you can display the information about the job:
Also after the job starts, you can list the datasets being processed by entering:
And you can monitor the job progress by entering:
This should give something like:
Because the dataset submitted consisted of trimmed reads, trimmed_fasta is the first column to have entries. When all entries under the stats column read "done," processing is finished.
If you did not use the "shutdown-when-done" argument when starting the daemon, you can stop it with the command:
See the section "Exploring Results" for how to access the results of your project.
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