update assembly

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diff --git a/_images/assembler-mapping.png b/_images/assembler-mapping.png
diff --git a/_images/assembler-runtimes.png b/_images/assembler-runtimes.png
diff --git a/_images/assembly.png b/_images/assembly.png
diff --git a/_images/read-vs-contig-alignment.png b/_images/read-vs-contig-alignment.png
diff --git a/assemble.md b/assemble.md
@@ -0,0 +1,97 @@
+# Run the MEGAHIT assembler
+
+[MEGAHIT](https://github.com/voutcn/megahit) is a very fast, quite
+good assembler designed for metagenomes.
+
+First, install some necessary software:
+
+```
+sudo apt-get update && \
+sudo apt-get install -y make libc6-dev g++ zlib1g-dev
+```
+
+Then, build the latest version of MEGAHIT:
+
+```
+cd ~/
+git clone https://github.com/voutcn/megahit.git
+cd megahit
+make
+```
+
+Now, download some data:
+
+```
+mkdir -p ~/data
+cd ~/data
+wget http://public.ged.msu.edu.s3.amazonaws.com/ecoli_ref-5m-trim.se.fq.gz
+wget http://public.ged.msu.edu.s3.amazonaws.com/ecoli_ref-5m-trim.pe.fq.gz
+```
+
+Now, finally, run the assembler!
+
+```
+mkdir ~/assembly
+cd ~/assembly
+ln -fs ../data/*.fq.gz .
+
+~/megahit/megahit --12 ecoli_ref-5m-trim.pe.fq.gz -r ecoli_ref-5m-trim.se.fq.gz -o ecoli -f
+```
+
+This will take about 2 minutes; at the end you should see output like
+this:
+
+```
+--- [STAT] 133 contigs, total 4567337 bp, min 212 bp, max 235645 bp, avg 34341 bp, N50 106391 bp
+--- [Tue May  9 12:53:45 2017] ALL DONE. Time elapsed: 127.323246 seconds ---
+```
+
+The output assembly will be in `ecoli/final.contigs.fa`.
+
+While the assembly runs...
+--------------------------
+
+Interpreting the MEGAHIT working output :)
+
+What does, and doesn't, assemble?
+
+How good is assembly anyway?
+
+Discussion:
+
+Why would we assemble, vs looking at raw reads?  What are the
+advantages and disadvantages?
+
+What are the technology tradeoffs between Illumina HiSeq, Illumina
+MiSeq, and PacBio? (Also see `this paper
+<http://ivory.idyll.org/blog/2015-sharon-paper.html>`__.)
+
+What kind of experimental design considerations should you have if you
+plan to assemble?
+
+Some figures: the first two come from work by Dr. Sherine Awad on
+analyzing the data from Shakya et al (2014).  The third comes from
+an analysis of read search vs contig search of a protein database.
+
+
+![runtimes](_images/assembler-runtimes.png)
+
+![mapping rates](_images/assembler-mapping.png)
+
+![read vs contig search](_images/read-vs-contig-alignment.png)
+
+## After the assembly is finished
+
+At this point we can do a bunch of things; see 
+
+* annotate the assembly;
+* evaluate the assembly's inclusion of k-mers and reads;
+* set up a BLAST database so that we can search it for genes of interest;
+* quantify the abundance of the contigs or genes in the assembly, using the original read data set;
+* if doing metagenomics, bin the contigs in the assembly into species bins;
+
+see [our other tutorials](https://2017-ucsc-metagenomics.readthedocs.io/en/latest/assemble.html#after-the-assembly-is-finished) for details!
+
+-----------------------------------------------
+
+[Return to index](index.html)
diff --git a/example.rst b/example.rst
diff --git a/index.md b/index.md
@@ -14,7 +14,7 @@ Command line, workflows, and Good Enough Practice
 
 How assembly works
 
-Actually running assembly!
+[Actually running assembly!](assemble.html)
 
 K-mers and sourmash for clustering samples.
 
diff --git a/toc.rst b/toc.rst
@@ -10,7 +10,7 @@ Put references to your files below:
    index
    aws/login-shell-win
    blast
-   example
+   assemble
 
 Indices and tables
 ==================