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

Evaluating assemblies with FRCbam

Assembly improvement using REAPR

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’.