lex-notes.txt

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

Enable HTTPS in the security group.

Install BWA
-----------

First, we need to install the `BWA aligner
<http://bio-bwa.sourceforge.net/>`__::

   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


Install samtools
----------------

Download and install samtools::

   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


Install 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 src/samtools;
   make
   cd ..
   cd ..
  ./configure
   make install



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
   perl -MCPAN -e 'install File::Spec::Link'

   ./install.sh

Install BioPython
-----------------

Do::

   pip install biopython

Install scaffoldgap2bed
-----------------------

do::

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


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

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

02_Mapping_reads_to_an_assembly

05_Evaluating_assemblies_with_FRCbam

08_Assembly_improvement_using_REAPR

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