2.5. Loading FASTA files

This command is mostly used to load the reference genome. The reference sequences are exclusively used to feed JBrowse.

If the reference sequences are really long (>200Mbp), there may be memory issues during the loading process and JBrowse may take too long to render the tracks. To avoid that, it’s possible to use the parameter (–nosequence) and configure JBrowse to get the reference data from a FASTA file.

2.5.1. Load FASTA

python manage.py load_fasta --file organism_chrs.fa --soterm chromosome --organism 'Arabidopsis thaliana'
  • Loading this file can be faster if you increase the number of threads (–cpu).
python manage.py load_fasta --help
–file FASTA File *
–organism Species name (eg. Homo sapiens, Mus musculus) *
–soterm SO Sequence Ontology Term (eg. chromosome, assembly) *
–description Description
–url URL
–doi DOI of a reference stored using load_publication (eg. 10.1111/s12122-012-1313-4)
–nosequence Don’t load the sequences
–cpu Number of threads

* required fields

2.5.2. Remove file

If, by any reason, you need to remove a fasta dataset you should use the command remove_file. If you delete a file, every record that depend on it will be deleted on cascade.

python manage.py remove_file --help
  • This command requires the file name (Dbxrefprop.value)