• File System
  ls — list items in current directory
  ls -l — list items in current directory and show in long format to see perimissions, size, and modification date
  ls -a — list all items in current directory, including hidden files
  ls -F — list all items in current directory and show directories with a slash and executables with a star
  ls dir — list all items in directory dir
  cd dir — change directory to dir
  cd .. — go up one directory
  cd / — go to the root directory
  cd ~ — go to to your home directory
  cd - — go to the last directory you were just in
  pwd — show present working directory
  mkdir dir — make directory dir
  rm file — remove file
  rm -r dir — remove directory dir recursively
  cp file1 file2 — copy file1 to file2
  cp -r dir1 dir2 — copy directory dir1 to dir2 recursively
  mv file1 file2 — move (rename) file1 to file2
  ln -s file link — create symbolic link to file
  touch file — create or update file
  cat file — output the contents of file
  less file — view file with page navigation
  head file — output the first 10 lines of file
  tail file — output the last 10 lines of file
  tail -f file — output the contents of file as it grows, starting with the last 10 lines
  vim file — edit file
  alias name 'command' — create an alias for a command
  
• System
  shutdown — shut down machine
  reboot — restart machine
  date — show the current date and time
  whoami — who you are logged in as
  finger user — display information about user
  man command — show the manual for command
  df — show disk usage
  du — show directory space usage
  free — show memory and swap usage
  whereis app — show possible locations of app
  which app — show which app will be run by default
  
• Process Management
  ps — display your currently active processes
  top — display all running processes
  kill pid — kill process id pid
  kill -9 pid — force kill process id pid
  
• Permissions
  ls -l — list items in current directory and show permissions
  chmod ugo file — change permissions of file to ugo - u is the user's permissions, g is the group's permissions, and o is everyone else's permissions. The values of u, g, and o can be any number between 0 and 7.
  7 — full permissions
  6 — read and write only
  5 — read and execute only
  4 — read only
  3 — write and execute only
  2 — write only
  1 — execute only
  0 — no permissions
  chmod 600 file — you can read and write - good for files
  chmod 700 file — you can read, write, and execute - good for scripts
  chmod 644 file — you can read and write, and everyone else can only read - good for web pages
  chmod 755 file — you can read, write, and execute, and everyone else can read and execute - good for programs that you want to share
  
• Networking
  wget file — download a file
  curl file — download a file
  scp user@host:file dir — secure copy a file from remote server to the dir directory on your machine
  scp file user@host:dir — secure copy a file from your machine to the dir directory on a remote server
  scp -r user@host:dir dir — secure copy the directory dir from remote server to the directory dir on your machine
  ssh user@host — connect to host as user
  ssh -p port user@host — connect to host on port as user
  ssh-copy-id user@host — add your key to host for user to enable a keyed or passwordless login
  ping host — ping host and output results
  whois domain — get information for domain
  dig domain — get DNS information for domain
  dig -x host — reverse lookup host
  lsof -i tcp:1337 — list all processes running on port 1337
  
• Searching
  grep pattern files — search for pattern in files
  grep -r pattern dir — search recursively for pattern in dir
  grep -rn pattern dir — search recursively for pattern in dir and show the line number found
  grep -r pattern dir --include='*.ext — search recursively for pattern in dir and only search in files with .ext extension
  command | grep pattern — search for pattern in the output of command
  find file — find all instances of file in real system
  locate file — find all instances of file using indexed database built from the updatedb command. Much faster than find
  sed -i 's/day/night/g' file — find all occurrences of day in a file and replace them with night - s means substitude and g means global - sed also supports regular expressions
  
• Compression
  tar cf file.tar files — create a tar named file.tar containing files
  tar xf file.tar — extract the files from file.tar
  tar czf file.tar.gz files — create a tar with Gzip compression
  tar xzf file.tar.gz — extract a tar using Gzip
  gzip file — compresses file and renames it to file.gz
  gzip -d file.gz — decompresses file.gz back to file
  
• Shortcuts
  ctrl+a — move cursor to beginning of line
  ctrl+f — move cursor to end of line
  alt+f — move cursor forward 1 word
  alt+b — move cursor backward 1 word
  

1. Accelrys Software Solution Pvt Ltd.
12th Floor, Discover, ITPL, White Field, Bangalore-65.
www.accelrys.com

2. Apticraft Systems (P) Ltd.
142, Electronics Complex, Pardeshipura, Indore – 452010 (M.P.), India
www.apticraft.com

3. Aptuit Informatics
Plot No. 100-103, Export Promotion Industrial Park, White Field, Bangalore-560066
www.aptiuit.com

4. Bigtec
J. K. Towers, 8th Block, Sangam Circle,46th Cross, Bangalore-560082.
www.bigtec.org

5. Bijam Biosciences Private Limited
Nagarjuna Hills, Hyderabad 500 082, India
www.nagarjunagroup.com

6. Bio Base Databases India Pvt Ltd.
Crescent Towers, 4th Floor, No : 32/1, Crescent Road, Bnagalore – 560 001
www.biobase-international.com

7. BioImagene India Pvt. Ltd.
4th floor, C-Wing, Godrej Eternia, Shivajinagar, Pune-411005
www.bioimagene.com

8. BioInformatics Institute Of India – Noida
C-56 A/28, Sector -62, Noida – 201 301
www.bii.in

9. CLC bio India Pvt Ltd
#Plot No. 51, H.No. 8-3-214/51, Srinivasa Nagar (West) Ameerpet Hyderabad – 500 038
www.clcbio.com/india

10. CytoGenomics India (P) Ltd.
#3004, 12A Main HAL 2nd Stage, Bangalore 560008
www.silicocyte.com

11. Genotypic Technology
211, 6th Cross, 80ft Road, RMV II Stage, Bangalore 560094
www.genotypic.co.in

12. Genvea Biosciences
Dr. D. T. Singh, CSO, 53, Craig Rd. #04-01, Singapore-089691
www.genvea.com

13. Helix Info Systems
132 A, II Floor, Sterling Towers, IV Cross Street, Sterling Road, Nungambakkam, Chennai.
www.helixinfosystems.com

14. Jalaja Technologies Pvt. Ltd.,
21/1,Victoria Layout, Victoria Road, Bangalore-47
www.jalaja.com

15. Jubilant Biosys Ltd
#96, Industrial Subrub, 2nd Stage, Yeshwanthpur, Bangalore- 560022
Jubilant Organosys Ltd.
1A, Sector 16A, Noida – 201 301 (India)
www.jubl.com

16. Kshema Technologies
#1, Global Village, Mylasandra, Mysore Road, Bangalore-560 059.
www.mphasis.com

17. LabNetworx
B-704, Gitanjali Apartments, Vikas Marg Extension, New Delhi – 110 092
www.labnetworx.com

18. LabVantage Solutions Pvt. Ltd.
Bengal Intelligent Park, Building C, 2nd Floor, Sector V, Salt Lake Electronics Complex, Kolkata – 700 091
www.labvantage.com

19. LeadInvent, 
2nd Floor, Biotech Centre, University of Delhi, South Campus, Benito Juarez Road, New Delhi 110021, India
Contact no: +91 11 24119241
Email: contact@leadinvent.com
www.leadinvent.com

20. Mascon Life Sciences
B – 8/ 10, Vasant Vihar, New Delhi 110057, India
www.masconlifesciences.com

21. Molecular Connections P Ltd
Kandala Mansion, 2/2 Kariappa Road, Near Krishna Rao Park, Basavangudi, Bangalore – 4
www.molecularconnections.com

22.Novo Informatics Pvt. Ltd.
TBIU, 2nd Floor, Synergy Building, Indian Institute of Technology, Hauz Khas, New Delhi-16.
Contact: 91-11-26581524, 91-11-26581766(Extension: 28)
Email: info@novoinformatics.com
www.novoinformatics.com

23. Ocimum Biosolutions (India) Ltd
6th Floor, Reliance Classic, Road No.1 Banjara Hills, Hyderabad 500 034, India.
www.ocimumbio.com

24. Scube Scientific Software Solutions
613, Hemkunt Chambers, 89, Nehru Place, New Delhi -110 019
www.scribeindia.com

25. Siri Technologies Pvt Ltd.
38/C -23, South End Road, Basavanagudi, Bangalore-56004.
www.siritech.com

26. Strand Life Sciences Pvt. Ltd.
#237, Sir C. V. Raman Avenue, Raj Mahal Vilas, Bangalore 560 080 INDIA
www.strandls.com

27. SooryaKiran Bioinformatics (P) Ltd
TBIC-13, Tejaswini Building, Technopark, Thriruvananthapuram- 695 584, Keralam, India

Ph: +91 471 4060979,+91 9895404104
Email: reachus@sooryakiran.com
http://www.sooryakiran.com

28. Systat Software Asia Pacific
4th Floor, Block 1, Shankar Narayan Building, No.25, MG Road, Bangalore – 560001
www.systat.com

29. ABC Genomics (India) Pvt. Ltd.
Biotech Park, Sector G, Jankipuram, Kursi Road, Lucknow-226021, U.P., INDIA
Tel +91-522-4068579, Email: director@abcgenomics.com
www.abcgenomics.com

30. en-GENE-ier's Core Technology Services,
1/340, Virat Khand, Gomtinagar, 
(Near Maharaja Agrasen Public School)
lucknow-226010, U.P., India.
http://www.bio.egicore.com/

Best of luck for your job hunts :).

https://academic.oup.com/bioinformatics/article/30/18/2559/2475628
Reference-free SNP detection: dealing with the data deluge

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4083407/
GATB/DiscoSnp: DiscoSnp is designed for discovering all kinds of SNPs (not only isolated ones), as well as insertions and deletions, from raw set(s) of reads.

https://github.com/GATB/DiscoSnp
De novo assembly | Oxford Nanopore Technologies

https://nanoporetech.com/taxonomy/term/131
De novo long-read assembly of a complex animal genome | bioRxiv

https://www.biorxiv.org/content/early/2017/09/10/187054
Rapid de novo assembly of the European eel genome from nanopore sequencing reads | Scientific Reports

https://www.nature.com/articles/s41598-017-07650-6.epdf?author_access_token=dktG7e98wyRJnaEEMTcPqtRgN0jAjWel9jnR3ZoTv0P7E7t-wVGo30iojNO7dICajNY_7PE5xVPv6OoLe7hn9TeUjcZ5umREOzNoPMWkfYH58RS6uxm3vm4e4BG2AA_WKW84i6egKK271NwMq-NfzA%3D%3D
nanoporetech/ont-assembly-polish: ONT assembly and Illumina polishing pipeline

https://github.com/nanoporetech/ont-assembly-polish
Generade-nl/TULIP: TULIP - The Uncorrected Long read Itegration Pipeline

https://github.com/Generade-nl/TULIP
www.nature.com

https://www.nature.com/articles/s41598-017-03996-z
Example gallery of NanoPlot – Gigabase or gigabyte

https://gigabaseorgigabyte.wordpress.com/2017/06/01/example-gallery-of-nanoplot/
Tool documentation

https://broadinstitute.github.io/picard/command-line-overview.html
Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. - PubMed - NCBI

https://www.ncbi.nlm.nih.gov/pubmed/24185095
MAFFT ver.7 - a multiple sequence alignment program

https://mafft.cbrc.jp/alignment/software/algorithms/algorithms.html
Measuring the distance between multiple sequence alignments | Bioinformatics | Oxford Academic

https://academic.oup.com/bioinformatics/article/28/4/495/212883
The MUMmer 3 examples

http://mummer.sourceforge.net/examples/
MAFFT ver.7 - a multiple sequence alignment program

https://mafft.cbrc.jp/alignment/software/tips.html
Omega | Overlap-graph de novo Assembler for Metagenomics

https://omega.omicsbio.org/
abiswas-odu/Disco: Multi-threaded Distributed Memory Overlap-Layout-Consensus (OLC) Metagenome Assembler

https://github.com/abiswas-odu/Disco
SAGE: String-overlap Assembly of GEnomes | BMC Bioinformatics | Full Text

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-302

Fast and sensitive mapping of nanopore sequencing reads with GraphMap | Nature Communications

https://www.nature.com/articles/ncomms11307
lumpy-sv/extractSplitReads_BwaMem at master · arq5x/lumpy-sv

https://github.com/arq5x/lumpy-sv/blob/master/scripts/extractSplitReads_BwaMem
jts/nanocorrect: Experimental pipeline for correcting nanopore reads

https://github.com/jts/nanocorrect

video - how to install flash plugin on ubuntu 14.04 LTS 64-bit version - Ask Ubuntu

https://askubuntu.com/questions/469553/how-to-install-flash-plugin-on-ubuntu-14-04-lts-64-bit-version
lh3/fermi: A WGS de novo assembler based on the FMD-index for large genomes

https://github.com/lh3/fermi
Multi-metagenome

http://madsalbertsen.github.io/multi-metagenome/docs/step9.html
Bandage by rrwick

https://rrwick.github.io/Bandage/
Codon Optimization OnLine (COOL): a web-based multi-objective optimization platform for synthetic gene design | Bioinformatics | Oxford Academic

https://academic.oup.com/bioinformatics/article/30/15/2210/2391162
Genome Architecture and Evolution of a Unichromosomal Asexual Nematode - ScienceDirect

https://www.sciencedirect.com/science/article/pii/S096098221731076X?via%3Dihub#fig4
How to determine chimeras in my de novo assembly? - SEQanswers

http://seqanswers.com/forums/showthread.php?t=26721
samtools(1) manual page

http://www.htslib.org/doc/samtools.html
How To Filter Mapped Reads With Samtools

https://www.biostars.org/p/56246/
The MUMmer 3 manual

http://mummer.sourceforge.net/manual/#nucmer
assembly_olc.pdf

http://www.cs.jhu.edu/~langmea/resources/lecture_notes/assembly_olc.pdf
SAM and BAM filtering oneliners

https://gist.github.com/davfre/8596159
Inroduction to dot-plots

http://www.code10.info/index.php%3Foption%3Dcom_content%26view%3Darticle%26id%3D64:inroduction-to-dot-plots%26catid%3D52:cat_coding_algorithms_dot-plots%26Itemid%3D76
RepeatFinder Home Page

http://www.cbcb.umd.edu/software/RepeatFinder/
RepeatFinderReprint.pdf

http://www.cbcb.umd.edu/software/RepeatFinder/RepeatFinderReprint.pdf
https://bernatgel.github.io/karyoploter_tutorial//Tutorial/CreateIdeogram/CreateIdeogram.html

https://bernatgel.github.io/karyoploter_tutorial//Tutorial/CreateIdeogram/CreateIdeogram.html
Circular Visualization in R

http://zuguang.de/circlize_book/book/introduction.html#a-qiuck-glance
Creating a coverage plot using BEDTools and R

https://davetang.org/muse/2015/08/05/creating-a-coverage-plot-using-bedtools-and-r/
Eval: A software package for analysis of genome annotations | BMC Bioinformatics | Full Text

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-4-50
eval-documentation.pdf

http://mblab.wustl.edu/media/software/eval-documentation.pdf
OmicCircos: A Simple-to-Use R Package for the Circular Visualization of Multidimensional Omics Data

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3921174/
sequence - download.tardigrades.org > v1 > sequence

http://download.tardigrades.org/v1/sequence/
ksahlin/BESST: BESST - scaffolder for genomic assemblies

https://github.com/ksahlin/BESST
reubwn/scripts: Useful scripts for various things

https://github.com/reubwn/scripts
ICEberg

http://db-mml.sjtu.edu.cn/ICEberg/index.php
Satsuma - Evolution and Genomics

http://evomics.org/learning/genomics/satsuma/
A complete bacterial genome assembled de novo using only nanopore sequencing data | Nature Methods

https://www.nature.com/articles/nmeth.3444
vezzi/FRC_align: Computes FRC from SAM/BAM file and not from afg files

https://mail.google.com/mail/u/0/#inbox
Read GTF file into R - Dave Tang's blog

https://davetang.org/muse/2017/08/04/read-gtf-file-r/

https://bernatgel.github.io/karyoploter_tutorial//Tutorial/CustomGenomes/CustomGenomes.html

https://bernatgel.github.io/karyoploter_tutorial//Tutorial/CustomGenomes/CustomGenomes.html
Dot: Interactive dot plot for genome-genome alignments

https://dnanexus.github.io/dot/
Zoho Accounts

https://accounts.zoho.eu/signin?servicename=ZohoProjects&serviceurl=https%3A%2F%2Fprojects.zoho.eu%2Fportal%2Favaga2
lh3/minimap2: A versatile pairwise aligner for genomic and spliced nucleotide sequences

https://github.com/lh3/minimap2
SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information | BMC Bioinformatics | Full Text

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-15-211
Palindromic gene amplification — an evolutionarily conserved role for DNA inverted repeats in the genome | Nature Reviews Cancer

https://www.nature.com/articles/nrc2591
bioinformatics - BLAST DNA Sequences Reversed - Biology Stack Exchange

https://biology.stackexchange.com/questions/8160/blast-dna-sequences-reversed
LASTZ

http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.02.00/README.lastz-1.02.00a.html
SOGo - (1652) Inbox

https://sogo.unamur.be/SOGo/so/jnarayan/Mail/view
Tetra-Nucleotide Analysis (TNA) | BIOiPLUG Help center

http://help.bioiplug.com/tetra-nucleotide-analysis-tna/

Clustering metagenomic contigs on tetranucleotide frequency — CGAT documentation

http://cgat.readthedocs.io/en/latest/recipes/metagenome_contigs_kmers.html

The project involves identification and characterization of transcription factors (TFs) from the Arabidopsis shoot apical meristem stem cell niche using genomic approaches and construction of a gene regulatory network for the identified TFs.

Positions: 1

Duration: 1 year but extendable up to three years based on performance and availability of funds.

Emoluments: As per DST rules.

Essential Qualifications: M.Sc. in any branch of life sciences with excellent academic record with CSIR-UGC NET or DBT-JRF. Candidate having previous work experience in the area of bioinformatics, molecular biology and genetics is preferred, but not required.

How to Apply: Applicants are requested to send a cover letter outlining previous research experiences and reasons for joining this position. Please send your complete bio-data including the cover letter as PDF attachment by email to Dr. Ram Yadav at ryadav@iisermohali.ac.in

Last date of submission is 17.00 IST, August 10, 2013.

Advertisement: www.iisermohali.ac.in/project_openings.html#29

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Genomics in India
www.ganitlabs.in
www.sandor.co.in
www.igib.res.in
www.genotypic.co.in
www.ocimumbio.com
www.abcgenomics.com
www.xcelrisgenomics.com
www.ayugen.com
www.geneombiotech.com

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 genomics platform uses cancer genome sequencing and other high-throughput techniques to identify genes critical to the development of cancer and anomalies in the genomic profile of the tumours.

For more info visit : http://oicr.on.ca/

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