===========
Assembly QC
===========

Enable HTTPS in the security group.

Installing software
-------------------

**BWA aligner**

Do::

   cd /root
   wget -O bwa-0.7.5.tar.bz2 http://sourceforge.net/projects/bio-bwa/files/bwa-0.7.5a.tar.bz2/download

   tar xvfj bwa-0.7.5.tar.bz2
   cd bwa-0.7.5a
   make

   cp bwa /usr/local/bin


**samtools**

Do::

   cd /root
   curl -L http://sourceforge.net/projects/samtools/files/latest/download?source=files >samtools.tar.bz2
   tar xjf samtools.tar.bz2
   mv samtools-* samtools-latest
   cd samtools-latest/
   make
   cp samtools bcftools/bcftools misc/* /usr/local/bin


**FRCAlign**

First::

   apt-get -y install libbz2-dev libboost-dev libboost-iostreams-dev libboost-program-options-dev libboost-thread-dev

Do::

   cd /root
   git clone https://github.com/vezzi/FRC_align
   cd FRC_align
   cd src/samtools;
   make
   cd ..
   cd ..
  ./configure
   make install



**REAPR**

Do::

   cd /root
   curl -O ftp://ftp.sanger.ac.uk/pub4/resources/software/reapr/Reapr_1.0.16.tar.gz
   tar xzf Reapr_1.0.16.tar.gz
   cd Reapr_1.0.16

   export PERL_MM_USE_DEFAULT=1
   export PERL_EXTUTILS_AUTOINSTALL=--defaultdeps
   export MAKEFLAGS='-j4'
   perl -MCPAN -e 'install File::Spec::Link'

   ./install.sh
   ln -s /root/Reapr_1.0.16/reapr /usr/local/bin/reapr

**Python modules**

Do::

   pip install biopython
   pip install pysam

**Install R**

Do::

   apt-get install r-base

**scaffoldgap2bed**

do::

   cd /usr/local/bin
   curl -O https://raw.github.com/lexnederbragt/sequencetools/master/scaffoldgap2bed.py
   chmod 770 scaffoldgap2bed.py

**An IPython notebook**

do::

   cd /usr/local/notebooks
   curl -O https://raw.github.com/lexnederbragt/INF-BIO9120_fall2013_de_novo_assembly/master/practicals/Plot_insertsizes.ipynb

Data files
----------

Create a new volume based on snapshot `snap-78cf1764` and attach it to your running instance via the Amazon EC2 management interface. When it is attached, remember the partition (e.g. sdf is `xvdf`) and mount like:

::

	mkdir /data2
	mount /dev/xvdf /data2

Practicals handouts
-------------------

Use the following practicals from https://github.com/lexnederbragt/INF-BIO9120_fall2013_de_novo_assembly/tree/master/practicals

`Mapping reads to an assembly <https://github.com/lexnederbragt/INF-BIO9120_fall2013_de_novo_assembly/blob/master/practicals/02_Mapping_reads_to_an_assembly.md>`__

`Evaluating assemblies with FRCbam <https://github.com/lexnederbragt/INF-BIO9120_fall2013_de_novo_assembly/tree/master/practicals/05_Evaluating_assemblies_with_FRCbam.md>`__

`Assembly improvement using REAPR <https://github.com/lexnederbragt/INF-BIO9120_fall2013_de_novo_assembly/tree/master/practicals/08_Assembly_improvement_using_REAPR.md>`__

Note that you'll have to adjust file paths and we're skipping a few
things (e.g. SNP calling)

Downloading data from the VM
----------------------------
use scp:

do::

   scp -i /path/to/keyfile.pem root@ec-xx-xx-xx-.compute-1.amazonaws.com:/path/to/data ./


For IGV, download:

* velvet fasta file
* bam and bai files
* bed and gff files once you have them

---

To connect to the IPython Notebook interface, connect to

   https://ec2-machine-name

(ignore/accept the security warning) and use the password 'beacon'.