Tools for working with genomic and high throughput sequencing data.
Group: FASTA
Collates the alternate contig names from an NCBI assembly report.
The input is to be the *.assembly_report.txt obtained from NCBI.
The output will be a “sequence dictionary”, which is a valid SAM file, containing the version header line and one
line per contig. The primary contig name (i.e. @SQ.SN) is specified with --primary option, while alternate
names (i.e. aliases) are specified with the --alternates option.
The Assigned-Molecule column, if specified as an --alternate, will only be used for sequences with
Sequence-Role assembled-molecule.
When updating an existing sequence dictionary with --existing the primary contig names must match. I.e. the
contig name from the assembly report column specified by --primary must match the contig name in the existing
sequence dictionary (@SQ.SN). All contigs in the existing sequence dictionary must be present in the assembly
report. Furthermore, contigs in the assembly report not found in the sequence dictionary will be ignored.
| Name | Flag | Type | Description | Required? | Max # of Values | Default Value(s) |
|---|---|---|---|---|---|---|
| input | i | FilePath | Input NCBI assembly report file. | Required | 1 | |
| output | o | PathToSequenceDictionary | Output sequence dictionary file. | Required | 1 | |
| primary | p | AssemblyReportColumn | The assembly report column for the primary contig name. | Optional | 1 | RefSeqAccession |
| alternates | a | AssemblyReportColumn | The assembly report column(s) for the alternate contig name(s) | Required | Unlimited | |
| sequence-roles | s | SequenceRole | Only output sequences with the given sequence roles. If none given, all sequences will be output. | Optional | Unlimited | |
| existing | d | PathToSequenceDictionary | Update an existing sequence dictionary file. The primary names must match. | Optional | 1 | |
| allow-mismatching-lengths | x | Boolean | Allow mismatching sequence lengths when using an existing sequence dictionary file. | Optional | 1 | false |
| skip-missing-alternates | Boolean | Skip contigs that have no alternates | Optional | 1 | true |