Update sequence alignment documentation

metagraph/docs/source/sequence_search.rst

@@ -38,17 +38,22 @@ flags are available.
 
 Sequence-to-graph alignment
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
+If the :code:`--map` flag is not used, this enables sequence-to-graph alignment, approximately finding the best-matching path in the graph to the query sequence. Alongside this path, this mode also returns an alignment score and a CIGAR string describing the edits needed to transform the spelling of the graph path to the query sequence. An example command may be::
 
-Additional parameters
-^^^^^^^^^^^^^^^^^^^^^
+    metagraph align -i MYGRAPH.dbg MYREADS.fa
 
-Query sequences against the index
----------------------------------
-(Experiment discovery)
+The output of the query is in TSV format, with one line per query sequence, where the columns are as follows:
 
-Parameters for exact k-mer matching
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+1. Query name
+2. Query sequence
+3. Strand
+4. Reference sequence (the spelling of the matched path
+5. Alignment score
+6. Number of exact matches
+7. CIGAR string-like alignment summary
+8. Number of nucleotides trimmed from the prefix of the reference sequence
+9. Ref name matches (if the :code:`-a` flag is passed)
 
-Parameters for alignment
-^^^^^^^^^^^^^^^^^^^^^^^^
+An important parameter is the seed length, which can be set with :code:`--align-min-seed-length` and can be shorter than the value of k used to construct the graph.
 
+If an annotator is provided with the :code:`-a` flag, the returned alignments will be label-consistent, meaning that there is at least one label that is shared by all nodes on the path.