# Reference FASTA

This is a required input file if the 'Custom' option is selected for 'Amplicon Primer Set'. This file contains one or more reference sequences as the target for short read alignment and as the basis for generating consensus sequences, but not all provided sequences may be used.

The file can contain sequences from multiple sources. For example, it can contain sequences of multiple segments from different Influenza genomes. In such cases, providing a corresponding Custom Reference BED file is highly recommended to inform the app which sequences should be belong together.

The app generates the required DRAGEN hash tables and other auxiliary files automatically, so there is no need to process the FASTA file with a separate app.

## Guidelines

* File name
  * Keep the file name short (<25 characters).
  * File extension must be .fasta or .fa (e.g. reference.fasta).
  * Avoid using spaces and use underscores (`_`) or hyphens (`-`) instead (e.g. reference\_01.fasta)
* Header
  * Header must start with `>` and contain a unique sequence name. If there is any space in the FASTA header, the part before the first space is assumed to be the sequence name.
  * Use the following in sequence names: alphabets, numbers, underscore (`_`), hyphen (`-`), parentheses (`(`,`)`), and period (`.`). Otherwise, the sequence names may appear different in the output.
  * Keep the sequence names short (e.g. sc2). If needed, longer names can be provided in the `genome` column of the Custom Reference BED.
  * If Custom Reference BED is provided, entries in its `accession` column must match the sequence names from this FASTA (any string before the first space in the header).
  * If Custom PCR Primer definition file is provided in BED-like format, entries in its `accession` column must match the sequence names from this FASTA (any string before the first space in the header).
* Sequence
  * Sequences must consist of the following characters: `A`, `C`, `T`, `G`, `N`, `R`, `Y`, `S`, `W`, `K`, `M`, `B`, `H`, `D`, `V`, `a`, `c`, `t`, `g`, `n`, `r`, `y`, `s`, `w`, `k`, `m`, `b`, `h`, `d`, `v`.
  * Other characters such as `-`, `_`, or `X` are not permitted and will result in error.
  * Do not include duplicate sequences.


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