Closes #200

docs/source/interpretation.rst

@@ -12,8 +12,8 @@ files and what they mean.
 Pipeline Stages
 ===============
 
-First we must get aquainted with the stages the pipeline runs.
-There are 5 stages available for the pipeline to run:
+First you should get aquainted with the stages the pipeline runs.
+There are 5 stages available for the pipeline to run in the order they are run:
 
 * :ref:`quality_analysis <quality-analysis-output-interpretation>`
 * :ref:`step1 <step1-output-interpretation>`
@@ -29,6 +29,43 @@ directory.
 General Interpretation
 ======================
 
+Here we will briefly list each stage and files that are most important. For a more
+detailed explenation of the stage and any relevant files generated, see the links
+above for each pipeline.
+
+* ray2_assembly_1
+
+    This stage is where all reads that did not get filtered due to host_map or
+    quality_filter will be denovo assembled into contigs.
+
+    Relevant files:
+
+        * 1.R1.unmap.fastq
+        * 1.R2.unmap.fastq
+        * out.cap.fa
+        * out.ray.fa
+
+    Relevant directories:
+
+        * reads_by_contig/
+
+* iterative_blast_phylo_1
+
+    This stage is where your ray assembled contigs will get blasted
+
+    Relevant files:
+
+        * reports/contig.*smallreport*.txt
+
+* iterative_blast_phylo_2
+
+    This is where the unassembled reads that passed host-map and quality filtering,
+    but did not map to any contigs in the ray assembly
+
+    Relevant files:
+
+        * reports/{R1,R2}.*smallreport*.txt
+
 Stage Output Read File
 ----------------------
 

docs/source/scripts/make_summary.rst

@@ -59,7 +59,7 @@ The contig report contains the following columns
 * numReads
     Number of reads supporting contig
     Gathered from ray2_assembly_1/contig_numreads.txt which comes
-   from the ray2_assembly_1/bowtie_mapping/out.bam by counting all mapped reads
+    from the ray2_assembly_1/bowtie_mapping/out.bam by counting all mapped reads
 * Accession, Family, Genus, description
     Blast information for contig