Tools for working with genomic and high throughput sequencing data.
Group: FASTA
Updates the sequence names in a FASTA.
The name of each sequence must match one of the names (including aliases) in the given sequence dictionary. The new name will be the primary (non-alias) name in the sequence dictionary.
By default, the sort order of the contigs will be the same as the input FASTA. Use the --sort-by-dict option to
sort by the input sequence dictionary. Furthermore, the sequence dictionary may contain more contigs than the
input FASTA, and they wont be used.
Use the --skip-missing option to skip contigs in the input FASTA that cannot be renamed (i.e. who are not present
in the input sequence dictionary); missing contigs will not be written to the output FASTA. Finally, use the
--default-contigs option to specify an additional FASTA which will be queried to locate contigs not present in
the input FASTA but present in the sequence dictionary.
| Name | Flag | Type | Description | Required? | Max # of Values | Default Value(s) |
|---|---|---|---|---|---|---|
| input | i | PathToFasta | Input FASTA. | Required | 1 | |
| dict | d | PathToSequenceDictionary | The path to the sequence dictionary with contig aliases. | Required | 1 | |
| output | o | PathToFasta | Output FASTA. | Required | 1 | |
| line-length | l | Int | Line length or sequence lines. | Optional | 1 | 100 |
| skip-missing | Boolean | Skip missing source contigs (will not be outputted). | Optional | 1 | false | |
| sort-by-dict | Boolean | Sort the contigs based on the input sequence dictionary. | Optional | 1 | false | |
| default-contigs | PathToFasta | Add sequences from this FASTA when contigs in the sequence dictionary are missing from the input FASTA. | Optional | 1 |