7  Conclusion

7.1 What we covered

In this session you have gone from opening a terminal for the first time to downloading and querying a real bacterial genome. Specifically, you can now:

  • Navigate a Unix file system using pwd, ls, cd, and mkdir
  • Create, copy, move and delete files and directories
  • Install command-line tools using package managers or installer scripts
  • Download sequences from NCBI using efetch or curl
  • Inspect biological files with head, tail, and less
  • Search for patterns with grep, count with wc, and chain commands with |

These are the building blocks of almost everything done in command-line bioinformatics.

7.2 Project organisation

Now that you can create directories and files from the command line, a natural next step is to think carefully about how to organise your work. A well-structured project is easier to reproduce, easier to share, and much easier to return to after six months away.

Noble (2009) (Noble 2009) describes a practical, widely adopted directory structure for computational biology projects, with separate directories for raw data, results, scripts, and documentation. It is a short, readable paper and strongly recommended.

7.3 Command reference

Command What it does
pwd Print working directory
ls List directory contents
cd Change directory
mkdir Make a new directory
touch Create an empty file
cp Copy a file or directory
mv Move or rename a file
rm Delete a file (-r for directories)
cat Print file contents
head Show first lines of a file
tail Show last lines of a file
less Scroll through a file
wc Count lines, words, characters
grep Search for patterns in files
echo Print text to the terminal
which Find where a programme is installed
man Open the manual for a command
esearch Search NCBI databases
efetch Fetch records from NCBI databases
curl Download files from URLs

7.4 Where to go next

The shell is deep. Here are some natural next steps depending on your goals.

If you want to go further with genomics:

If you want to write scripts:

Start with a simple bash script: a file ending in .sh containing the commands you would type interactively. Add a for loop when you need to repeat a task across multiple files.

If you need to work on a remote server (HPC):

  • ssh username@server.address connects to a remote machine
  • scp or rsync copy files to and from a remote machine
  • SLURM or PBS are the job schedulers most commonly used on university HPC clusters

7.5 Acknowledgements

This workshop is adapted from the Data Carpentry shell genomics lesson (Becker et al. 2019) and Clara Jégousse’s previous workshops.