Assembly QC

Enable HTTPS in the security group.

Installing software

BWA aligner


cd /root
wget -O bwa-0.7.5.tar.bz2

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

cp bwa /usr/local/bin



cd /root
curl -L >samtools.tar.bz2
tar xjf samtools.tar.bz2
mv samtools-* samtools-latest
cd samtools-latest/
cp samtools bcftools/bcftools misc/* /usr/local/bin



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


 cd /root
 git clone
 cd FRC_align
 cd src/samtools;
 cd ..
 cd ..
 make install



cd /root
curl -O
tar xzf Reapr_1.0.16.tar.gz
cd Reapr_1.0.16

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

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

Python modules


pip install biopython
pip install pysam

Install R


apt-get install r-base



cd /usr/local/bin
curl -O
chmod 770

An IPython notebook


cd /usr/local/notebooks
curl -O

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

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:


scp -i /path/to/keyfile.pem ./

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

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

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LICENSE: This documentation and all textual/graphic site content is licensed under the Creative Commons - 0 License (CC0) -- fork @ github. Presentations (PPT/PDF) and PDFs are the property of their respective owners and are under the terms indicated within the presentation.

Development and posting of this material, and the associated workshop, were supported by Grant Number R25HG006243 from the National Human Genome Research Institute and an NSF OCI supplement to NSF DBI-0939454.

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