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1. Reference construction

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Benedikt Kuhnhäuser edited this page Jun 23, 2026 · 10 revisions

GPID requires a reference directory containing BLAST databases for all genes used for identification.

To construct this reference directory, provide a directory with one FASTA file per gene, each containing sequences of all reference samples.

Formatting Requirements

First, check that your gene and sample names follow the formatting requirements:

  • Gene sequences need to be unaligned and in .FNA, .fasta or .fa format.
  • Gene names need to match the gene names in the test dataset.
  • Each reference sample name needs to start with genus and species name <Genus>_<species>, followed by a unique identifier for the sample.
  • Use underscores _ as separators in the sample names.
  • Sample names in each file need to be identical.

Example contents of reference directory

Gene1.FNA:

>Entandrophragma_angolense_CQL_22
CTCCCATATAGGGGTGCTTGGTTGTGGGTGGGTTCTGAGATGATTCATTTAATGGAACTT
CCAAATCCAGATCCCTTAACTGGACGACCGGCACATGGTGGTCGAGATCGTCATACTTGT
ATTGCGATTCGAGATGTGTCTAAACTCAAAATAATCCTTGATAAAGCAGGTATTCCTTAC
>Entandrophragma_bussei_CQL_EB42
CTCCCATATAGGGGTGCTTGGTTGTGGGTGGGTTCTGAGATGATTCATTTAATGGAACTT
CCAAATCCAGACCCCTTAACTGGACGACCGGCACATGGTGGTCGAGATCGTCATACTTGT
ATTGCGATTCGAGATGTGTCTAAACTCAAAATAATCCTTGATAAAGCAGGTATTCCTTAC
>Entandrophragma_candollei_CQL_13
CTTCCGTATAGGGGTGCTTGGTTGTGGGTGGGTTCTGAGATGATTCATTTAATGGAACTT
CCAAATCCAGACCCCTTAACGGGACGACCGGCACATGGTGGTCGAGATCGTCATACTTGT
ATTGCGATTCGAGATGTGTCTAAACTGAAAATAATCCTTGACAAAGCAGGTGTTCCTTAC

Gene2.FNA:

>Entandrophragma_angolense_CQL_22
GTTGGGGATCTACACGGAGACCTTGATCAAGCGAGATGTGCACTTGAGATTGCTGGTGTC
>Entandrophragma_bussei_CQL_EB42
GTTGGGGATCTACACGGAGACCTTGATCAAGCGAGATGTGCACTTGAGATTGCTGGTGTC
>Entandrophragma_candollei_CQL_13
GCTGGGGATCTACATGGAGACCTTGATCAAGCAAGATGTGCACTTGAGATTGCTGGTGTC

Gene3.FNA:

>Entandrophragma_angolense_CQL_22
GAATCTCAAGGATTAACATCTCGACGATTGTGTCTTACATGTATATGTTCAACTCTAGCT
CTGATTAACAGTTCCGGCACGTTGGTTTCTGTACAAAAGGCAATTGCTTTGGAAGGAAAA
>Entandrophragma_bussei_CQL_EB42
GATATGTGTGGTGGTACAGGAAAATGGAAAGCTCTCAACAGAAAACGTGCTAAAGATGTT
TACGAGTTTACAGAATGTCCAAATTGTTATGGTCGTGGGAAACTTGTGTGTCCGGTTTGC
>Entandrophragma_candollei_CQL_13
GAATCTCAGATATCAACATCTCGCCGTTGGTGCCTTACGTGTATACTTACATGTATATGT
TCAACTCTAGCTCTGATTAACAGTTCCGGCACATTGGTTTCTGTACAAAAGGCAATTGCT

Reference construction

Now build the reference using:
gpid reference -r <reference directory>

Options:
-r Path to the reference directory containing all genes with reference samples
-h Show help message

This command performs the following steps:

  1. locating FASTA files (.FNA, .fasta, .fa)
  2. validating FASTA header format
  3. checking whether BLAST databases already exist
  4. building missing BLAST databases with makeblastdb

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