HPG Aligner README
Welcome to HPG Aligner!
HPG Aligner is an ultrafast and highly sensitive Next-Generation Sequencing (NGS) read mapping.
hpg-aligner - The executable file to map DNA/RNA sequences
CONTACT
You can contact any of the following developers:
* Joaquín Tárraga (jtarraga@cipf.es)
* Héctor Martínez (martineh@icc.uji.es)
* Ignacio Medina (imedina@cipf.es)HPG Aligner has been opened to the community and released in GitHub, so you can download by invoking the following commands:
$ git clone https://github.com/opencb/hpg-aligner.git
Cloning into 'hpg-aligner'...
remote: Reusing existing pack: 1441, done.
remote: Total 1441 (delta 0), reused 0 (delta 0)
Receiving objects: 100% (1441/1441), 1.85 MiB | 122 KiB/s, done.
Resolving deltas: 100% (882/882), done.
$ cd hpg-aligner
$ git submodule update --init
Submodule 'lib/hpg-libs' (https://github.com/opencb/hpg-libs.git) registered for path 'lib/hpg-libs'
Cloning into 'lib/hpg-libs'...
remote: Reusing existing pack: 7735, done.
remote: Total 7735 (delta 0), reused 0 (delta 0)
Receiving objects: 100% (7735/7735), 26.82 MiB | 79 KiB/s, done.
Resolving deltas: 100% (4430/4430), done.
Submodule path 'lib/hpg-libs': checked out '962f531ef0ffa2a6a665ae6fba8bc2337c4351a9'You can see the available HPG Aligner releases by using the command:
$ git tag
v2.0.0
v2.0.1Select the HPG Aligner relesase you want to use, for instance,
$ git checkout v2.0.1Before building the HPG Aligner, you must install on your system the following packages: git, gcc, scons, zlib, curl, xml, curses, gsl and check.
In Ubuntu and Debian distributions, you can install them by using theses commands:
$ apt-get install git
$ apt-get install gcc
$ apt-get install scons
$ apt-get install zlib1g-dev libcurl4-gnutls-dev libxml2-dev libncurses5-dev libgsl0-dev checkAnd in Centos and Fedora distributions:
$ yum install git
$ yum install gcc
$ yum install scons
$ yum install zlib-devel libcurl-devel libxml2-devel ncurses-devel gsl-devel check-develFinally, use Scons to build the HPG Aligner application:
$ sconsFor command line options invoke:
$ ./bin/hpg-aligner -hIn order to map DNA sequences:
1) Create the HPG Aligner index based on suffix arrays by invoking:
$ ./bin/hpg-aligner build-sa-index -g <ref-genome-fasta-file> -i <index-directory>
Example:
$./bin/hpg-aligner build-sa-index -g /hpg/genome/human/GRCH_37_ens73.fa -i /tmp/sa-index-human73/
2) Map by invoking:
$./bin/hpg-aligner dna -i <index-directory> -f <fastq-file> -o <output-directory>
Example:
$./bin/hpg-aligner dna -i /tmp/sa-index-human73/ -f /hpg/fastq/simulated/human/DNA/GRCh37_ens73/4M_100nt_r0.01.bwa.read1.fastq
----------------------------------------------
Loading SA tables...
End of loading SA tables in 1.03 min. Done!!
----------------------------------------------
Starting mapping...
End of mapping in 1.40 min. Done!!
----------------------------------------------
Output file : hpg_aligner_output/alignments.sam
Num. reads : 4000000
Num. mapped reads : 3994693 (99.87 %)
Num. unmapped reads: 5307 (0.13 %)
----------------------------------------------In order to map RNA sequences:
A) Map Based on Burrows-Wheeler Transform method for slow memory consumption
1) Create the BWT HPG Aligner index
$ ./bin/hpg-aligner build-bwt-index -g <ref-genome-fasta-file> -i <index-directory> -r <compression-ratio>
Example:
$ ./bin/hpg-aligner build-bwt-index -g /home/user/Homo_sapiens.fa -i /home/user/INDEX/ -r 8
2) Map by invoking:
$ ./bin/hpg-aligner rna -i <index-directory> -f <fastq-file> -o <output-directory>
Example:
$ ./bin/hpg-aligner rna -i /home/user/INDEX/ -f reads.fq
+===============================================================+
| RNA MODE |
+===============================================================+
| ___ ___ ___ |
| \/ H \/ P \/ G \/ |
| /\___/\___/\___/\ |
| ___ ___ ___ ___ ___ ___ ___ |
| \/ A \/ L \/ I \/ G \/ N \/ E \/ R \/ |
| /\___/\___/\___/\___/\___/\___/\___/\ |
| |
+===============================================================+
WORKFLOW 1
[|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||] 100%
WORKFLOW 2
[|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||] 100%
WORKFLOW 3
[|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||] 100%
+===============================================================+
| H P G - A L I G N E R S T A T I S T I C S |
+===============================================================+
| T I M E S T A T I S T I C S |
+---------------------------------------------------------------+
Loading time : 5.69 (s)
Alignment time : 438.09 (s)
Total time : 443.79 (s)
+---------------------------------------------------------------+
| M A P P I N G S T A T I S T I C S |
+---------------------------------------------------------------+
Total reads process : 10000000
Total reads mapped : 9977505 (99.78%)
Total reads unmapped : 22495 (0.22%)
Reads with a single mapping : 9532383 (95.32%)
Reads with multi mappings : 445122 (4.45%)
Reads mapped with BWT phase : 6441691 (64.42%)
Reads mapped in workflow 1 : 9737937 (97.38%)
Reads mapped in workflow 2 : 149381 (1.49%)
Reads mapped in workflow 3 : 90187 (0.90%)
+---------------------------------------------------------------+
| S P L I C E J U N C T I O N S S T A T I S T I C S |
+---------------------------------------------------------------+
Total splice junctions : 2556653
Total cannonical splice junctions : 2535847 (99.19%)
Total semi-cannonical splice junctions : 20806 (0.81%)
+---------------------------------------------------------------+
B) Map Based on SA method for more speed
1) Create the SA HPG Aligner index
$ ./bin/hpg-aligner build-sa-index -g <ref-genome-fasta-file> -i <index-directory>
Example:
$./bin/hpg-aligner build-sa-index -g /home/user/Homo_sapiens.fa -i /home/user/INDEX/
2) Map by invoking:
$ ./bin/hpg-aligner rna -i <index-directory> -f <fastq-file> -o <output-directory> --sa-mode
Example:
$ ./bin/hpg-aligner rna -i /home/user/INDEX/ -f reads.fq -o /home/user/sa_output --sa-modeYou can find more info about HPG Aligner project at: