The prepint version is found on http://www.biorxiv.org/content/early/2017/08/09/173872

It uses the pyPaSWAS framework for sequence alignment (https://github.com/swarris/pyPaSWAS)

Address of the bookmark: https://github.com/swarris/Pacasus

https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2017/Day1/Session4-seqIntro.html

Address of the bookmark: https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2017/Day1/Session4-seqIntro.html

Many times in bioinformatics we need to deal with huge datasets which  are more than 100GB size. The traditional way to analysis a file is using the while loop

while (FILE){

Do something;

}

This is very slow(since we are using only one processor) and if we have 500 million lines in the dataset it takes more than a day to iterate through the whole dataset. So how do we make best use of all our processors and get the work done quickly?

Here is a very simple and efficient technique with perl which i have been using. I am  more inclined towards using perl fork than perl threads.

One of the oldest way to fork is

my $fork = fork();
if($fork){   
push (@childs,$fork); 
}
elseif($fork==0){
your code here;
exit(0);
}
else{die “Couldnt fork : $!”;}

## wait for the child process to finish
foreach(@childs){
my $tmp=waitid($_,0);
}

what a fork does is it creates a child process and takes the variables and code with it to analyze it separately (detached from the parent process) and thus a separate process is created( which usually runs on a separate processor). Thats it!! One big disadvantage of forking is its very difficult to share variables among the different processes. I will show you how to do it easily but still it has its own drawbacks.

Okie, now if you really do not want to use fork in your code, that’s okie too..There are many useful modules which do it for you very efficiently. One really useful module is Parallel::ForkManager. You can use Parallel::ForkManager to manage the number of forks you want to generate (number of processors you want to use).

Simple usage:
use Parallel::ForkManager;
my $max_processors=8;
my $fork= new Parallel::ForkManager($max_processors);
foreach (@dna) {
$fork->start and next; # do the fork
you code here;
$fork->finish; # do the exit in the child process
}
$pm->wait_all_children;

so you will be generating 8 forks which do the same thing for your each element of array. when one child finishes, Parallel::ForkManager generates a new one and thus you will be using all your processors to analyze the data. Now, if you have generated 8 child processes and want to write the data to one file. You need to lock the file to do this, because you will have problems with the buffering. You can lock the file using flock command.

open (my $QUAL, “myfile.txt”);
flock $QUAL, LOCK_EX or die “cant lock file $!”;
print $QUAL “$output”;
flock $QUAL, LOCK_UN or die “$!”;
close $QUAL;

I would not suggest using flock when dealing with multiple processes because it will decrease the processing efficiency( each child process must wait for the lock to be released by the other child process). Instead, I would suggest each fork writing to a separate file and after the processing just concatenating them.

Putting it all together, If you have 100GB data you can do this

step 1 : split the dataset equally according to number of processors you have. this may take a few hours(about 2-3 hrs for 100GB file)
You can use unix “split” command for this
for example:
my $number_split=int($number_of_entries_in_your_dataset/$max_processors);
my $split_Files=`split -l $number_split “your_file.fasta” “file_name”`;

step2: open you directory comtaining you split files and start Parallel::ForkManager.
For example:
opendir(DIRECTORY, $split_files_directory) or die $!; ### open the directory
my $fork= new Parallel::ForkManager($max_processors);
while (my $file = readdir(DIRECTORY)) { ### read the directory
if($file=~/^\./){next;}
print $file,”\n”;
########## Start fork ##########
my $pid= $super_fork->start and next;
Whatever you want to do with the split file ;
analyze my piece of $file;
######### end fork ###############
$super_fork->finish;
}
$super_fork->wait_all_children;

So basically each processor will be active with its piece of data (split file) and thus you have created 8 processes at one time which run without interfering with the other process. I again will not suggest writing output from each child process to one file(for reasons above). Write output from each fork to a separate file and finally concatenate them. Thats it, you have just increased your program speed by 8 times!! Isnt it easy?

Note:
You may worry about concatenation of the output each child generates, since it does take some time(remember 100GB). I think now you can use a mysql database LOAD DATA LOCAL INFILE command to load all the files into a single table(Should take about 3hrs for 100Gb dataset) and then export the whole table into one file. This should be faster than just concatenating them using “cat” command.(correct me if I am wrong)

Or much simpler way is to use pipes

cat output_dir/* | my_pipe or my_pipe <(file1) final_file;

Thats it guys!! Enjoy programming and please do comment. I am not a computer scientist so forgive me for any mistakes and if any please report them. Thank you.

Source: Life technologies

Address of the bookmark: http://www.lifetechnologies.com/global/en/home/communities-social/blog/blogs/sequencing-solutions-to-world-health.html?cid=social_blogseries_20130829_11098264

Title: Comparison of Short Read De Novo Alignment Algorithms 

Author: Nikhil Gopal

Address of the bookmark: http://biochem218.stanford.edu/Projects%202011/Gopal%202011.pdf

http://bmi.osu.edu/hpc/software/benchmark/

http://bmi.osu.edu/hpc/software/pmap/pmap.html

Other similiar papers:

http://online.liebertpub.com/doi/pdf/10.1089/cmb.2012.0022

http://bioinformatics.oxfordjournals.org/content/28/24/3169

Some new Mapping tool links:

GSNAP

http://research-pub.gene.com/gmap/

RMAP

http://rulai.cshl.edu/rmap/

mrsFAST

http://mrsfast.sourceforge.net/Home

http://sourceforge.net/projects/mrsfast/files/mrsfast-ultra-3.1.0/

BFAST

http://sourceforge.net/apps/mediawiki/bfast/index.php?title=Main_Page

SHRiMP (for AB SOLiD color-space reads)

http://compbio.cs.toronto.edu/shrimp/

RazerA 3

http://www.seqan.de/projects/razers/

Address of the bookmark: http://www.biomedcentral.com/1471-2105/14/184

Related Paper:

http://genomebiology.com/2014/15/3/R59/abstract

Address of the bookmark: http://www.news.ucdavis.edu/search/news_detail.lasso?id=10859

Tool link:

http://www.cs.cmu.edu/~ckingsf/software/sailfish/

Address of the bookmark: http://www.genengnews.com/gen-news-highlights/lightweight-algorithms-sail-through-rna-sequencing-data/81249765/

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