Update docs on reference annotation

Closes #88
mgalardini · Sep 5, 2019 · 565c363 · 565c363
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diff --git a/docs/tutorial.rst b/docs/tutorial.rst
@@ -384,7 +384,8 @@ a single type of each annotation, but this could be expanded by adding all
 the annotated assemblies to the input.
 
 We'll start by creating a ``references.txt`` file listing the annotations we
-wish to use::
+wish to use (see :ref:`annotate-kmers` for more information on how to construct
+this file)::
 
    Spn23F.fa	Spn23F.gff	ref
    6952_7#3.fa	6952_7#3.gff	draft

diff --git a/docs/usage.rst b/docs/usage.rst
@@ -595,6 +595,8 @@ as its position. The y-axis is :math:`-\mathrm{log}_{10}(p)`.
    a real time interface, so we recommend filtering out those with a p-value
    below a threshold value for interactive performance.
 
+.. _annotate-kmers:
+
 Annotating k-mers
 ^^^^^^^^^^^^^^^^^
 
@@ -617,6 +619,10 @@ references to be used::
    sample1.fa	sample1.gff	draft
    sample2.fa	sample2.gff	draft
 
+To map all of the k-mers, and ensure good quality annotation where possible, provide
+a few trusted references as the first lines in this file. You can then list all of the assemblies
+used as input after this, designated as draft.
+
 For each k-mer, each match will be returned in the format 'contig:pos;gene_down;gene_in;gene_up'
 i.e. the closest downstream gene, the gene the k-mer is in (if it is), the closest
 upstream gene. The gene name will be chosen if in the GFF, otherwise the gene