sed ':a;N;$!ba;s/\n//g' filename.txt > newfilename_oneline.txt

To get average for a column of numbers (here the second column $2):

awk '{ sum += $2; n++ } END { if (n > 0) print sum / n; }'

To get sequence length for all sequences in a fasta file:

awk '/^>/ {if (seqlen){print seqlen}; print ;seqlen=0;next; } { seqlen = seqlen +length($0)}END{print seqlen}' \
filename.fasta

To copy (move, rename, etc) files based on their list in a text file:

cat file_list.txt | while read line; do cp "$line" complete_dataset/"$line"; done

To split bam files into sets with mapped and unmapped reads:

samtools view -F4 sample.bam > sample.mapped.sam
samtools view -f4 sample.bam > sample.unmapped.sam

To gzip all your fastq files using gnu parallel and gzip:

parallel gzip ::: *.fastq

To gzip all your fastq files using pigz:

pigz *.fastq

To count all sequences in a fasta file:

grep "^>" yourfile.fasta -c

To count all sequences in all fasta files in your current directory:

for a in *.fasta; do ls $a; grep "^>" -c $a; done

To keep only one copy of duplicated lines:

awk '!seen[$0]++'

To sum assembly size from SPAdes contigs.fasta or scaffolds.fasta file:

grep "^>" scaffolds.fasta | cut -f 4 -d '_' | paste -sd+ | bc

To remove everything after the first space at each line, e.g. to to simplify fasta headers:

cut -d' ' -f1 < your_file

To count reads in a all .fastq.gz files in your current folder (fast, using gnu parallel):

parallel "echo {} && gunzip -c {} | wc -l | awk '{d=\$1; print d/4;}'" ::: *.gz

To count reads in a all .fastq.gz files in your current folder:

zcat *.gz | echo $((`wc -l`/4))

To count reads in a all .fastq files in your current folder:

cat *.fastq | echo $((`wc -l`/4))

To count base pairs in a all .fastq.gz files in your current folder:

zcat *.fastq.gz | paste - - - - | cut -f 2 | tr -d '\n' | wc -c 

To split multifasta file into many fasta files:

awk '/^>/ {OUT=substr($0,2) ".fa"}; {print >> OUT; close(OUT)}' Input_File

To convert Illumina FASTQ 1.3 to 1.8:

sed -e '4~4y/@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\\]^_`abcdefghi/!"#$%&'\''()*+,-.\/0123456789:;<=>?@ABCDEFGHIJ/' f.fastq

To convert FASTQ to FASTA:

sed -n '1~4s/^@/>/p;2~4p' 

To get fastq read length distribution:

cat reads.fastq | awk '{if(NR%4==2) print length($1)}' | sort | uniq -c

To deinterleave interleaved fastq file:

cat myf.fq | paste - - - - - - - - | tee >(cut -f 1-4 | tr "\t" "\n" > myfile_1.fq) | cut -f 5-8 | \
tr "\t" "\n" > myf2.fq 

To filter and sort contig identifiers from SPAdes assembly (e.g. here lenght >= 4000 + coverage >=100):

grep "^>" scaffolds.fasta | sed s"/_/ /"g | awk '{ if ($4 >= 4000 && $6 >= 100) print $0 }' | sort -k 4 -n | \
sed s"/ /_/"g

To append something to all headers of your fasta files:

sed 's/>.*/&YOURSTRING/' filename.fasta > new_filename.fasta

To replace/squeeze multiple adjacent spaces by only one space: 

tr -s " " < file

To filter fastq based on length (here larger than or equal to 21, but smaller than or equal to 25.

cat your.fastq | paste - - - - | awk 'length($2)  >= 21 && length($2) <= 25' | sed 's/\t/\n/g' > filtered.fastq

To print difference between the last and first row in 5th column:

awk '{if (!first){first=$5;}; last=$5;} END {print last-first}' myfile.txt

To sample only 200 first bases from all sequences in a multifasta file (e.g. from assembly scaffolds.fasta file here):

awk '/^>/{ seqlen=0; print; next; } seqlen < 200 { if (seqlen + length($0) > 200) $0 = substr($0, 1, 200-seqlen);\
 seqlen += length($0); print }' scaffolds.fasta > 200bp_scaffolds.fasta

 To pipe a compressed fasta file directly into makeblastdb.

gunzip -c fasta.gz | makeblastdb -in -

To remove sequences with duplicate fasta headers from a fasta file.

awk '/^>/{f=!d[$1];d[$1]=1}f' in.fasta > out.fasta

Pockets Identification

CASTp

Pocket-Finder

PocketPicker

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.

The data are available using NCBI accession IDs: BioProject: (PRJNA483067), assembly: [RBJD00000000] and sequence data (SRP155659).

Additional Resources

• Interactive map showcasing global initiatives underway to generate reference-quality human genome assemblies for diverse populations
• BioReport Podcast on the value of ethnic-specific reference genomes
• Nature Reviews Genetics paper from NHGRI: Prioritizing diversity in human genomics research
• Article in The Journal of Precision Medicine: “Minority Report – Ethnic Diversity and the Real Promise for Precision Medicine”
• Article in Bio-IT World: “Genomic Data Standards Are a Necessity”
• NHGRI Project Award: High Quality Human and Non-Human Primate Genome Assemblies

More details are available on the PacBio website:

• Blog post: Data Release: Highest-Quality, Most Contiguous Individual Human Genome Assembly to Date
• Blog post: For Reference-Grade Human Genome Assemblies, SMRT Sequencing Yields Optimal Results
• Webinar:  Assembling High-Quality Human Reference Genomes for Global Populations
• FALCON-Phase press release and article preprint
• PacBio research focus webpage about Human Population Genetics

 Ref: https://stockguru.com/2018/10/08/pacific-biosciences-releases-highest-quality-most-contiguous-individual-human-genome-assembly-to-date/

Requirements
- 3-5 years of relevant bioinformatics experience such as public data mining,
processing, analysing and visualising omics data, etc.
- Ph.D., Masters or Bachelors in Bioinformatics, Biotechnology,
Computational Biology, or related field.
- Understanding of molecular biology and biochemistry.
- Comfort and experience with biological research and data.
- Proficient in a programming language used for bioinformatics such as R or
python.
- Excellent communication skills.
- Ability to summarise and simplify complex analyses for a non-technical
audience.
- Strong analytical skills, curiosity and a knack to solve difficult problems.
- Work well in multi-disciplinary teams with people of vastly different
backgrounds.
- Demonstrated success in collaboration and independent work.

More at https://angel.co/elucidata/jobs/460104-senior-bioinformatics-scientist

RaGOO is a tool for coalescing genome assembly contigs into pseudochromosomes via minimap2 alignments to a closely related reference genome. The focus of this tool is on practicality and therefore has the following features:

1. Good performance. On a MacBook Pro using Arabidopsis data, pseudochromosome construction takes less than a minute and the whole pipeline with SV calling takes ~2 minutes.
2. Intact ordering and orienting of contigs.
3. Chimeric contig correction
4. GFF lift-over
5. Structural variant calling with and integrated version of Assemblytics
6. Confidence scores associated with the grouping, localization, and orientation for each contig.

Address of the bookmark: https://github.com/malonge/RaGOO

Also, Bioinformatics Industrial Training Program (BIITP) is merged with the HRD Biotechnology Industrial Training Programme (BITP).

While this comes as a surprise for a lot of participants. We believe this is a good attempt to unify and create a national benchmark for talent. And we appreciate this endeavor from Department of biotechnology.

However, such last-minute announcements can create confusion. Thus candidates are advised to go through the complete notification DBT-BET JRF 2019 via the link below.If you have any kind of doubts, you must contact DBT JRF or Biotecnika for any kind of help & assistance.

Attention:-Bioinformatics Programs (BINC and BIITP)

1. Bioinformatics National Certification (BINC) has been merged with DBT-Junior
Research Fellow (BET Exam)

2. Bioinformatics Industrial Training Program (BIITP) is merged with HRDBiotechnology Industrial Training Programme (BITP).

Students of Bioinformatics, who are interested to apply for Fellowship or Industrial
Training may keep track of the advertisement of DBT-JRF (BET Exam) and BITP
of DBT.

 More at http://www.bcil.nic.in/files/Attention_Bioinformatics_Programs_(BINC_and_BIITP).pdf

More at https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa179/5804978?rss=1

Address of the bookmark: https://github.com/CMU-SAFARI/Apollo

No previous programming knowledge is assumed. By following this tutorial you will learn the fundamental concepts of programming by using scripting languages: variables, types, arrays, cycles, conditional statements, functions, objects, regular expressions, files reading and manipulation et-cetera.

Address of the bookmark: http://www.cellbiol.com/bioinformatics_web_development/introduction/