Screen is like a window manager for your console. It will allow you to keep multiple terminal sessions running and easily switch between them. It also protects you from disconnection, because the screen session doesn’t end when you get disconnected.

You’ll need to make sure that screen is installed on the server you are connecting to. If that server is Ubuntu or Debian, just use this command:

sudo apt-get install screen

Now you can start a new screen session by just typing screen at the command line. You’ll be shown some information about screen. Hit enter, and you’ll be at a normal prompt.

To disconnect (but leave the session running)

Hit Ctrl + A and then Ctrl + D in immediate succession. You will see the message [detached]

To reconnect to an already running session

screen -r

To reconnect to an existing session, or create a new one if none exists

screen -D -r

To create a new window inside of a running screen session

Hit Ctrl + A and then C in immediate succession. You will see a new prompt.

To switch from one screen window to another

Hit Ctrl + A and then Ctrl + A in immediate succession.

To list open screen windows

Hit Ctrl + A and then W in immediate succession

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'du' – Check the size of a directory

$ du
This command ( du) gives you a list of directories that exist in the current working directory along with their sizes in kilobytes (default). The last line of the output gives you the total size of the current directory including its subdirectories.

$ du /home/jin1
The above command would give you the directory size of the directory /home/david

$ du -h
The same “du”command with some flag gives you a better output than the default one. The option '-h' stands for human readable format. Therefore, in order to print the sizes of the files / directories in your desire notation use this time suffixed with a 'k' if its kilobytes and 'M' if its Megabytes and 'G' if its Gigabytes.

$ du -ah
If you are interested in checking everything present in a folder use above mentioned command. It gives us not only the directories but also all the files that are present in the current directory. The “-a” flag displays the filenames along with the directory names in the output.

$ du -c
This gives you a grand total as the last line of the output. So if your directory occupies 30MB the last 2 lines of the output would be 30M.

$ du -s
Use this command to displays a summary of the directory size. It is the simplest way to know the total size of the current directory.

$ du -S
This would display the size of the current directory excluding the size of the subdirectories that exist within that directory. So it basically shows you the total size of all the files that exist in the current directory.

$ du --exculde=mp3
Several times it required to exclude some directory in our size calculation. In such cases the above command would display the size of the current directory along with all its subdirectories, but it would exclude all the files having the given pattern present in their filenames.

'df' - finding the disk free space / disk usage

$ df
Hmmm … now “df” command is really useful, and I guess you are going to use it over time. Typing the above command, outputs a table consisting of 6 columns. All the columns are very easy to understand. Remember that the 'Size', 'Used' and 'Avail' columns use kilobytes as the unit. The 'Use%' column shows the usage as a percentage which is also very useful.

$ df -h
Displays the same output as the previous command but the '-h' indicates human readable format. Hence instead of kilobytes as the unit the output would have 'M' for Megabytes and 'G' for Gigabytes.

Example: Linux installed on /dev/hda1
$ df -h | grep /dev/hda1

All right, this is not the only option to check the sizes and free spaces but there are a few more options that can be used with 'du' and 'df' . I will discuss it later.

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(details of experience required)
Pay Scale:
INR Rs.12000/-P.M. + HRA
Category:
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How To Apply:
The interested candidates should report for the Interview on 31st
March, 2014 at 10:00 am in the Conference Room of Dean, School of Biotechnology, First floor, Gautam Buddha University, Greater
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Download Official Notification:

http://www.gbu.ac.in/Recruitment/JRF_advertisement_DSTProject_Shakti_24March14.pdf

The fellowship will be for a period of 3 years, or for a period of 4 years, with 25 % compulsory work (e.g. teaching responsibilities at the department) contingent on the qualifications of the candidate and the teaching needs of the department.

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Part I – Basic Find Commands for Finding Files with Names
1. Find Files Using Name in Current Directory

Find all the files whose name is gene.txt in a current working directory.

# find . -name gene.txt

./gene.txt

2. Find Files Under Home Directory

Find all the files under /home directory with name gene.txt.

# find /home -name gene.txt

/home/gene.txt

3. Find Files Using Name and Ignoring Case

Find all the files whose name is gene.txt and contains both capital and small letters in /home directory.

# find /home -iname gene.txt

./gene.txt
./Gene.txt

4. Find Directories Using Name

Find all directories whose name is Gene in / directory.

# find / -type d -name Gene

/Gene

5. Find fasta Files Using Name

Find all php files whose name is gene.fasta in a current working directory.

# find . -type f -name gene.fasta

./gene.fasta

6. Find all PHP Files in Directory

Find all fasta files in a directory.

# find . -type f -name "*.fasta"

./gene.fasta
./cancer.fasta
./allgene.fasta

Part II – Find Files Based on their Permissions
7. Find Files With 777 Permissions

Find all the files whose permissions are 777.

# find . -type f -perm 0777 -print

8. Find Files Without 777 Permissions

Find all the files without permission 777.

# find / -type f ! -perm 777

9. Find SGID Files with 644 Permissions

Find all the SGID bit files whose permissions set to 644.

# find / -perm 2644

10. Find Sticky Bit Files with 551 Permissions

Find all the Sticky Bit set files whose permission are 551.

# find / -perm 1551

11. Find SUID Files

Find all SUID set files.

# find / -perm /u=s

12. Find SGID Files

Find all SGID set files.

# find / -perm /g+s

13. Find Read Only Files

Find all Read Only files.

# find / -perm /u=r

14. Find Executable Files

Find all Executable files.

# find / -perm /a=x

15. Find Files with 777 Permissions and Chmod to 644

Find all 777 permission files and use chmod command to set permissions to 644.

# find / -type f -perm 0777 -print -exec chmod 644 {} \;

16. Find Directories with 777 Permissions and Chmod to 755

Find all 777 permission directories and use chmod command to set permissions to 755.

# find / -type d -perm 777 -print -exec chmod 755 {} \;

17. Find and remove single File

To find a single file called gene.txt and remove it.

# find . -type f -name "gene.txt" -exec rm -f {} \;

18. Find and remove Multiple File

To find and remove multiple files such as .fa or .gb, then use.

# find . -type f -name "*.fa" -exec rm -f {} \;

OR

# find . -type f -name "*.gb" -exec rm -f {} \;

19. Find all Empty Files

To file all empty files under certain path.

# find /tmp -type f -empty

20. Find all Empty Directories

To file all empty directories under certain path.

# find /tmp -type d -empty

21. File all Hidden Files

To find all hidden files, use below command.

# find /tmp -type f -name ".*"

Part III – Search Files Based On Owners and Groups
22. Find Single File Based on User

To find all or single file called gene.txt under / root directory of owner root.

# find / -user root -name gene.txt

23. Find all Files Based on User

To find all files that belongs to user Rahul under /home directory.

# find /home -user rahul

24. Find all Files Based on Group

To find all files that belongs to group Developer under /home directory.

# find /home -group developer

25. Find Particular Files of User

To find all .txt files of user Rahul under /home directory.

# find /home -user rahul -iname "*.txt"

Part IV – Find Files and Directories Based on Date and Time
26. Find Last 50 Days Modified Files

To find all the files which are modified 50 days back.

# find / -mtime 50

27. Find Last 50 Days Accessed Files

To find all the files which are accessed 50 days back.

# find / -atime 50

28. Find Last 50-100 Days Modified Files

To find all the files which are modified more than 50 days back and less than 100 days.

# find / -mtime +50 –mtime -100

29. Find Changed Files in Last 1 Hour

To find all the files which are changed in last 1 hour.

# find / -cmin -60

30. Find Modified Files in Last 1 Hour

To find all the files which are modified in last 1 hour.

# find / -mmin -60

31. Find Accessed Files in Last 1 Hour

To find all the files which are accessed in last 1 hour.

# find / -amin -60

Part V – Find Files and Directories Based on Size
32. Find 50MB Files

To find all 50MB files, use.

# find / -size 50M

33. Find Size between 50MB – 100MB

To find all the files which are greater than 50MB and less than 100MB.

# find / -size +50M -size -100M

34. Find and Delete 100MB Files

To find all 100MB files and delete them using one single command.

# find / -size +100M -exec rm -rf {} \;

35. Find Specific Files and Delete

Find all .gb files with more than 10MB and delete them using one single command.

# find / -type f -name *.gb -size +10M -exec rm {} \;

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1. SPAdes: An assembler specifically designed for single-cell and multi-cell bacterial genomes, as well as small eukaryotic genomes.

2. ABySS: A parallelized assembler for large genomes that uses de Bruijn graphs.

3. Velvet: Another de Bruijn graph-based assembler optimized for short-read sequencing data.

4. SOAPdenovo: A de Bruijn graph-based assembler designed for short reads, widely used for assembling large and complex genomes.

5. MaSuRCA: A hybrid assembler that combines data from multiple sequencing technologies, such as Illumina and PacBio.

6. Canu: A long-read assembler optimized for PacBio and Oxford Nanopore sequencing data.

7. Flye: A long-read assembler suitable for bacterial and small eukaryotic genomes.

8. SMARTdenovo: An assembler designed for long reads, particularly suited for PacBio data.

9. SPAdes Long Read (SPAdesLR): An extension of SPAdes for long-read data, such as those from PacBio or Nanopore.

10. Minia: An assembler optimized for low memory consumption, suitable for small and medium-sized genomes.

11. Unicycler: A hybrid assembler that combines short and long reads for circular bacterial genome assembly.

12. wtdbg2: A de Bruijn graph assembler for long reads, efficient for very large genomes.

13. Shasta: A long-read assembler that uses the Overlap-Layout-Consensus approach, suitable for PacBio and Nanopore data.

14. Sparc: An assembler designed to handle noisy long reads from Nanopore sequencing.

15. CANA: An assembler for metagenomic data, particularly for complex and diverse microbial communities.

16. Ra Assembler: A metagenome assembler for long reads, designed for highly complex metagenomic samples.

Please note that the field of bioinformatics is constantly evolving, and new assembly tools may have emerged since my last update. Additionally, the performance of these tools can vary depending on the characteristics of the sequencing data and the genome being assembled. When selecting an assembly tool, consider the specific requirements of your project, the available data types, and the computational resources at your disposal. Always refer to the respective tool's documentation and publications for the most up-to-date information and recommendations.