Informatics on High-Throughput Sequencing Data

Post Workshop Access and Instructions

Additional Training on Git and Data Management

Software Carpentry has Version control with Git lesson - http://swcarpentry.github.io/git-novice/

Data Carpentry has Data management for Genomics lesson - https://datacarpentry.org/organization-genomics

Docker Container

Docker container from Mathieu Bourgey is here:

To set up using Docker:

mkdir ~/cvmfs_cache
docker run --privileged -v /tmp:/tmp --network host -it -w $PWD -v $HOME:$HOME  -v ~/cvmfs_cache:/cvmfs-cache/    c3genomics/genpipes:0.7

Data Sets

The data sets in the workshop can be downloaded from below. If your download speed is slow, please contact zhibin<at>gmail.com who can provide you with the alternative methods.

AWS Image

The AWS AMI for 2019 CBW workshop is publicly avaiable at US East region. AMI name: CBW_2019, AMI ID: ami-0b3a39967ade13fbb. Please let us know if you need it in other regions.

Tools and Installation Instructions

bioperl

sudo apt install expat
perl -MCPAN -e shell
install Module::Build
o conf prefer_installer MB
o conf commit
d /bioperl/
install CJFIELDS/BioPerl-1.007002.tar.gz

R

add “deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/” into /etc/apt/sources.list.d/R.list

sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
sudo apt update
sudo apt-get install r-base r-base-dev

abyss

sudo apt-get install abyss

bam-readcount

git clone https://github.com/genome/bam-readcount.git
cmake bam-readcount/
make

bamtools

git clone git://github.com/pezmaster31/bamtools.git
cd bamtools
mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX=/usr/local ..
make
sudo make install

bedops

wget https://github.com/bedops/bedops/releases/download/v2.4.35/bedops_linux_x86_64-v2.4.35.tar.bz2
tar -jxf bedops_linux_x86_64-v2.4.35.tar.bz2

bedtools

wget https://github.com/arq5x/bedtools2/releases/download/v2.27.1/bedtools-2.27.1.tar.gz
tar zxf bedtools-2.27.1.tar.gz
cd bedtools2/
make
sudo make install

blast+

wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.8.1+-x64-linux.tar.gz
tar zxf ncbi-blast-2.8.1+-x64-linux.tar.gz

bowtie2

wget http://cfhcable.dl.sourceforge.net/project/bowtie-bio/bowtie2/2.3.4.3/bowtie2-2.3.4.3-linux-x86_64.zip
unzip bowtie2-2.3.4.3-linux-x86_64.zip

bwa

wget https://newcontinuum.dl.sourceforge.net/project/bio-bwa/bwa-0.7.17.tar.bz2
tar -jxvf bwa-0.7.17.tar.bz2
cd bwa-0.7.17/
make

canu

wget wget https://github.com/marbl/canu/releases/download/v1.8/canu-1.8.Linux-amd64.tar.xz
xz -dv canu-1.8.Linux-amd64.tar.xz
tar -xvf canu-1.8.Linux-amd64.tar

Centrifuge

wget https://github.com/infphilo/centrifuge/archive/v1.0.4-beta.tar.gz
tar zxf v1.0.4-beta.tar.gz
cd centrifuge-1.0.4-beta/
make

DELLY

wget https://github.com/dellytools/delly/releases/download/v0.8.1/delly_v0.8.1_linux_x86_64bit
mv delly_v0.8.1_linux_x86_64bit delly
chmod +x delly

FastQC

wget http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.8.zip
unzip fastqc_v0.11.8.zip
cd FastQC
chmod +x fastqc

Note: if you get error: Exception in thread “Thread-1” java.awt.AWTError: Assistive Technology not found: org.GNOME.Accessibility.AtkWrapper You can comment out the following line in /etc/java-8-openjdk/accessibility.properties

assistive_technologies=org.GNOME.Accessibility.AtkWrapper

or run the following before you run fastqc

export _JAVA_OPTIONS=-Djavax.accessibility.assistive_technologies=

Flexbar

sudo apt install flexbar

GATK

download from https://www.broadinstitute.org/gatk/download (need to log in)
unzip gatk-4.1.0.0.zip

gffcompare

wget http://ccb.jhu.edu/software/stringtie/dl/gffcompare-0.10.6.Linux_x86_64.tar.gz
tar zxf gffcompare-0.10.6.Linux_x86_64.tar.gz

GMAP

wget http://research-pub.gene.com/gmap/src/gmap-gsnap-2018-07-04.tar.gz
tar -zxf gmap-gsnap-2018-07-04.tar.gz
cd gmap-2018-07-04
./configure
make
sudo make install

HISAT2

wget http://ccb.jhu.edu/software/hisat2/dl/hisat2-2.1.0-Linux_x86_64.zip
unzip hisat2-2.1.0-Linux_x86_64.zip && rm hisat2-2.1.0-Linux_x86_64.zip

HMMER

wget http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2-linux-intel-x86_64.tar.gz
tar zxf hmmer-3.1b2-linux-intel-x86_64.tar.gz

HTSeq

sudo pip install HTSeq

JellyFish

wget https://github.com/gmarcais/Jellyfish/releases/download/v2.2.10/jellyfish-linux
chmod +x jellyfish-linux

kallisto

wget https://github.com/pachterlab/kallisto/releases/download/v0.45.0/kallisto_linux-v0.45.0.tar.gz
tar zxf kallisto_linux-v0.45.0.tar.gz

medaka

need to modify medaka_variant and medaka_consensus to use python3 because the system default python is version 2.

sudo pip3 install medaka

minimap2

curl -L https://github.com/lh3/minimap2/releases/download/v2.16/minimap2-2.16_x64-linux.tar.bz2 | tar -jxvf -
./minimap2-2.16_x64-linux/minimap2

MultiQC

pip install multiqc

Picard

wget https://github.com/broadinstitute/picard/releases/download/2.18.26/picard.jar

pilon

wget https://github.com/broadinstitute/pilon/releases/download/v1.23/pilon-1.23.jar

QUAST

wget wget https://downloads.sourceforge.net/project/quast/quast-5.0.2.tar.gz
python ./setup.py build
sudo python ./setup.py install

racon

wget https://github.com/isovic/racon/releases/download/1.3.2/racon-v1.3.2.tar.gz
tar zxf racon-v1.3.2.tar.gz
cd racon-v1.3.2/
mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=Release ..
make

regtools

wget https://github.com/griffithlab/regtools/archive/0.5.0.tar.gz
cd regtools-0.5.0
mkdir build
cd build/
cmake ..
make

RSEM

wget https://github.com/deweylab/RSEM/archive/v1.3.1.tar.gz
tar zxf v1.3.1.tar.gz
cd RSEM-1.3.1/
make
sudo make ebseq (need ‘blockmodeling’, ‘testthat’ R packages)
sudo make install

RSeQC

sudo pip install RSeQC

Salmon

wget https://github.com/COMBINE-lab/salmon/releases/download/v0.12.0/salmon-0.12.0_linux_x86_64.tar.gz
tar xzf salmon-0.12.0_linux_x86_64.tar.gz

SAMStat

needs samtools to be installed first.

wget http://downloads.sourceforge.net/project/samstat/samstat-1.5.1.tar.gz
tar -xzvf samstat-1.5.1.tar.gz
cd samstat-1.5.1/
./configure
make
sudo make install

samtools

wget https://downloads.sourceforge.net/project/samtools/samtools/1.9/samtools-1.9.tar.bz2
tar -jxvf samtools-1.9.tar.bz2
cd samtools-1.9
make
sudo make install

snpEff

wget https://downloads.sourceforge.net/project/snpeff/snpEff_latest_core.zip
unzip snpEff_latest_core.zip

SPAdas

wget http://cab.spbu.ru/files/release3.13.0/SPAdes-3.13.0-Linux.tar.gz
tar xvf SPAdes-3.13.0-Linux.tar.gz

STAR

wget https://github.com/alexdobin/STAR/archive/2.7.0c.tar.gz
tar -xzf 2.7.0c.tar.gz

STAR-Fusion

wget https://github.com/STAR-Fusion/STAR-Fusion/releases/download/STAR-Fusion-v1.5.0/STAR-Fusion-v1.5.0.FULL.tar.gz
tar zxf STAR-Fusion-v1.5.0.FULL.tar.gz

Strelka

wget https://github.com/Illumina/strelka/releases/download/v2.9.10/strelka-2.9.10.release_src.tar.bz2
tar -jxf strelka-2.9.10.release_src.tar.bz2
cd strelka-2.9.10.release_src
mkdir build && cd build
../configure
make -C .
sudo make install
put /usr/local/libexec into PATH

stringtie

wget http://ccb.jhu.edu/software/stringtie/dl/stringtie-1.3.5.Linux_x86_64.tar.gz
tar zxf stringtie-1.3.5.Linux_x86_64.tar.gz

tophat

wget https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.Linux_x86_64.tar.gz
tar -zxf tophat-2.1.1.Linux_x86_64.tar.gz

TransDecoder

wget https://github.com/TransDecoder/TransDecoder/archive/TransDecoder-v5.5.0.tar.gz
tar zxf TransDecoder-v5.5.0.tar.gz

Trimmomatic

wget http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.38.zip
unzip Trimmomatic-0.38.zip

Trinity

wget https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v2.8.4.tar.gz
tar -zxvf Trinity-v2.8.4.tar.gz
cd trinityrnaseq-Trinity-v2.8.4
make
make plugins

Trinotate

wget https://github.com/Trinotate/Trinotate/archive/Trinotate-v3.1.1.tar.gz
tar zxf Trinotate-v3.1.1.tar.gz