added assembly

ngs-docs · Oct 11, 2016 · b3114e7 · b3114e7
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diff --git a/assemble.rst b/assemble.rst
@@ -0,0 +1,19 @@
+Run the MEGAHIT assembler
+=========================
+
+Assemble! ::
+
+   cd
+   git clone https://github.com/voutcn/megahit.git
+   cd megahit
+   make
+
+   cd /mnt/data
+   curl -O https://s3-us-west-1.amazonaws.com/dib-training.ucdavis.edu/metagenomics-scripps-2016-10-12/SRR1976948.abundtrim.subset.pe.fq.gz
+   curl -O https://s3-us-west-1.amazonaws.com/dib-training.ucdavis.edu/metagenomics-scripps-2016-10-12/SRR1977249.abundtrim.subset.pe.fq.gz
+
+   mkdir /mnt/assembly
+   cd /mnt/assembly
+   ln -fs ../data/*.subset.pe.fq.gz .
+
+   ~/megahit/megahit --12 SRR1976948.abundtrim.subset.pe.fq.gz,SRR1977249.abundtrim.subset.pe.fq.gz -o combined
diff --git a/index.rst b/index.rst
@@ -42,6 +42,7 @@ Tutorials:
    welcome
    aws/index
    quality
+   assemble
 
 Technical information
 ~~~~~~~~~~~~~~~~~~~~~

diff --git a/quality.rst b/quality.rst
@@ -243,4 +243,4 @@ Questions:
 
 Optional: trim
 
-Next: :doc:`n-assemble`
+Next: :doc:`assemble`