Skip to content

Latest commit

 

History

History
52 lines (37 loc) · 3.11 KB

input_files.md

File metadata and controls

52 lines (37 loc) · 3.11 KB
Raw

Icon Input files

TypeLoader accepts sequences for => New Alleles in either of two formats:

  • Fasta format
  • XML format produced by NGSEngine (GenDX)

Sequence Requirements

See => Sequence Requirements to check the minimum requirements for TypeLoader's input sequences.

Fasta files

Fasta files should contain exactly one sequence. (If they contain more than that, only the first sequence is used. To add multiple fasta sequences at once, use the => Bulk Fasta Upload.)

important The files MUST follow FASTA format conventions! (see further below)

important For KIR alleles, the locus MUST be provided! (see directly below) Otherwise, TypeLoader will try and fail to map your allele against the HLA database.

Optionally, you can use the sequence header to pass further data along to TypeLoader, which it will then store for your allele. This should be a list of key-value pairs separated by ";", like in this example:

fasta-header example

The following keys are currently recognized:

  • locus
  • ref, second, third, fourth (all of these allele names are concatenated with 'or' and stored as "partner_allele")
  • LIMS_DONOR_ID or SAMPLE_ID_INT (internal sample ID)
  • Spendernummer or SAMPLE_ID_EXT (external sample ID)
  • notes (comment)
  • short_read_data (was short-read data used to generate this sequence, yes/no?)
  • short_read_type (type of short reads used)
  • long_read_data (was long-read data used to generate this sequence, yes/no?)
  • long_read_type (type of long reads used)
  • software (software used for full-length genotyping)
  • version (version of the software used for full-length genotyping)
  • date (date of secondary genotyping)
  • customer (customer who provided the sample)
  • provenance (country in which the sample was taken)
  • collection_date (timestamp at which the sample was taken; must comply to ISO8601)

Fasta file format

Fasta files are standard text files for sequences. The first line is the header and starts with a ">" followed by the name of the sequence (any name will do) and any additional information separated by a space (see above). The second line and all following lines contain the actual sequence, which ends if the file ends or the next header starts, whichever happens first.

fasta-header example

Recognized file endings are .fa and .fasta.

XML files

The XML file exported from NSGEngine contains both alleles of one locus of one sample. If you upload such a file to TypeLoader, the dialog will ask you to clarify which of the alleles you want to add. (If you want to add both alleles, run the => New Allele Dialog twice with the same file, and choose the other allele during the second run.)

Example files

TypeLoader provides => example sequences in fasta format for all gene systems, so you can have a look at the format TypeLoader expects.