Insert

For most ciliate species, MAC genome data and reference assemblies are more readily available than MIC genome data. For certain analyses, it is useful to have a reference sequence containing IESs (IES+, or MAC+IES), if a MIC genome is not available.

To facilitate this, the Insert utility module allows users to artificially insert IES sequences into a MAC reference genome from a GFF3 file and a Fasta of the corresponding IES sequences, to obtain the MAC+IES reference and a GFF3 file of the updated IES coordinates (--mode insert). The utility also permits the reverse operation (--mode delete).

Input data

The inputs required are a Fasta file containing the reference genome (supplied to --fasta option), and GFF3 file of IES junction/region coordinates (--ies).

In insert mode (--mode insert), an additional Fasta file of the IES sequences is required, supplied to the --iesfasta option. The headers in this Fasta file should correspond to the ID value in the attributes field of the IES GFF file.

If the genome has existing annotations in a GFF3 feature table, this can be supplied to the --featuregff option. The coordinates of the annotations will be updated after the insertion of IESs, and other annotation fields remain unchanged. If a feature is interrupted by one or more IESs, the feature will be split into two or more features. If the feature contains an ID attribute and the option --addsuffix is chosen, then the ID of the original feature is suffixed with .seg_0, .seg_1 et seq. to distinguish the different segments split from the original entry. By default the ID field is unchanged. The updating of an existing feature table is only available in insert mode, because the deletion or truncation of an existing feature annotation will require manual intervention or curation.

Output

If run in insert mode (--mode insert), IES sequences are inserted into the MAC genome to produce a hybrid MAC+IES reference, with the following files:

• {OUT}.iesplus.fasta - Fasta file containing MAC+IES reference
• {OUT}.iesplus.gff - GFF file containing updated coordinates for the inserted IES sequences, derived from the input GFF file of IES junctions.

If run in delete mode (--mode delete), IES sequences are removed from the MAC+IES (or MIC) genome to produce a MAC-like reference, with the following files:

• {OUT}.iesminus.fasta - Fasta file containing IES- reference
• {OUT}.iesminus.gff - GFF file containing updated coordinates for the removed IES sequences, derived from the input GFF file of IES regions.