Set up NGS aligner

1. MAQ

source: http://sourceforge.net/projects/maq/files/maq/

cd /home/leiz/NGS/downloads
wget http://sourceforge.net/projects/maq/files/maq/0.7.1/maq-0.7.1.tar.bz2/download
tar -jxvf maq-0.7.1.tar.bz2
cd maq-0.7.1
./configure --prefix=/home/leiz/NGS/maq-0.7.1
make
make install



2. BWA
source: http://bio-bwa.sourceforge.net/

cd /home/leiz/NGS
wget http://sourceforge.net/projects/bio-bwa/files/bwa-0.5.9.tar.bz2/download
tar -jxvf bwa-0.5.9.tar.bz2
cd bwa-0.5.9
make



3. bowtie
source: http://bowtie-bio.sourceforge.net/index.shtml

cd /home/leiz/NGS

wget http://sourceforge.net/projects/bowtie-bio/files/bowtie/0.12.7/bowtie-0.12.7-linux-x86_64.zip/download

unzip bowtie-0.12.7-linux-x86_64.zip 

bowtie-0.12.7

./bowtie


#copy hg19.fa to bowtie index folder
cp ./hg19.fa ../bowtie-0.12.7/indexes/
 nohup bowtie-build ./hg19.fa ../bowtie-0.12.7/indexes/hg19 >screen.txt &

cd ../bowtie-0.12.7/indexes/hg19

bowtie-inspect --summary hg19

vi $HOME/.bashrc 

# User specific aliases and functions

export BOWTIE_INDEXES=/home/leiz/NGS/bowtie-0.12.7/indexes/

source $HOME/.bashrc 

 bowtie -c hg19 ATGACGGCGGCCGAGAAGTTGGATTTCTTGGT

nohup tophat -r 200  --num-threads=4 hg19 AGS_1_sequence.fastq  AGS_2_sequence.fastq >screen.txt &

4. samtools

source: http://sourceforge.net/projects/samtools/files/samtools/

cd /home/leiz/NGS/downloads
wget http://sourceforge.net/projects/samtools/files/samtools/0.1.16/samtools-0.1.16.tar.bz2/download
tar -jxvf samtools-0.1.16.tar.bz2
cd  samtools-0.1.16
mv samtools-0.1.16 .. 
make

5. picard
java 1.6 need: http://www.java.com/en/download/manual.jsp
cd /home/leiz/java

wget http://javadl.sun.com/webapps/download/AutoDL?BundleId=48338 -O jre-6u25-linux-x64.bin

chmod a+x jre-6u25-linux-x64.bin

./

jre-6u25-linux-x64.bin

add java path /home/leiz/java/jre1.6.0_25/bin to $PATH in .bash_profile
source .bash_profile
java -version

source: 

http://sourceforge.net/projects/picard/files/

cd /home/leiz/NGS/downloads
wget http://sourceforge.net/projects/picard/files/picard-tools/1.44/picard-tools-1.44.zip/download
unzip picard-tools-1.44.zipmv picard-tools-1.44 .. 

6. cufflinks

http://sourceforge.net/projects/boost/files/boost/1.46.1/boost_1_46_1.zip/download
wget http://cufflinks.cbcb.umd.edu/downloads/cufflinks-0.9.3.Linux_x86_64.tar.gz
http://cufflinks.cbcb.umd.edu/downloads/test_data.sam
cufflinks ./test_data.sam