From 53152089413d64e0066ded3c75cac894fe3a0d50 Mon Sep 17 00:00:00 2001
From: chris Mitchell <chris@ginkgobioworks.com>
Date: Wed, 23 Oct 2024 09:54:04 -0400
Subject: [PATCH] Add docs

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+# Paths and Accessions
+
+Graphs have particular challenges when it comes to referring to regions within one. For example, take the following
+chromosome and a simple change to it:
+
+```mermaid
+flowchart LR
+    A[ATCG] --> B[AAA] --> C[TTT]
+    A --> D[A] --> C
+  
+```
+
+If we specified an insertion at position 6, would it refer to `ATCGA_A_` or `ATCGA_T_`? Paths offer a mechanism
+to provide a linear sequence through a graph. Paths are an ordered series of edges that provide a mechanism for 
+addressing the space within a graph. For example, we could assign `Chr1` to the graph in the following manner:
+
+```mermaid
+flowchart LR
+    A[ATCG] -->|chr1| B[AAA] -->|chr1| C[TTT]
+    A --> D[A] --> C
+```
+
+and thus provide a reference frame for modifications. On fasta import, each header automatically becomes a defined path,
+so `Chr1` and so on will be automatically assigned.
+
+## Accessions
+
+When inserting changes to a genome, we may want to refer to the modifications. For example, in the above change, we have
+no way to refer to the `A` node. Accessions allow us to provide an addressable subspace within the graph. This is 
+especially useful for a stable reference to a sub-sequence such as a gene of interest or a landing pad, as iterative 
+changes to the genome may alter its relative position.  
+
+To illustrate this, suppose we are inserting a small landing pad into a genome.
+
+```mermaid
+flowchart LR
+    A[ATCG] -->|chr1| B[AAA] -->|chr1| C[TTT]
+    A -->|landing-pad| D[CCC] -->|landing-pad| C
+```
+
+Now, suppose in a downstream sample we insert a sequence before the landing pad.
+
+```mermaid
+flowchart LR
+    E[GGG] -->|chr1| A
+    A[ATCG] -->|chr1| B[AAA] -->|chr1| C[TTT]
+    A -->|landing-pad| D[CCC] -->|landing-pad| C
+```
+
+While chr1's length has changed, `landing-pad`'s coordinates have not. This permits operations to simply refer to 
+`landing-pad` instead of knowing the chromosomal coordinates of the landing pad.
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