index.qmd

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title: "Home"
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# Introduction

The objective of this tutorial is to learn *de novo* genome assembly for relatively small genomes (e.g. Fungii).

This resource will provide you with the basic concepts in *de novo* genome assembly from and will distinguish three critical step for analysis.

-   Primary analysis: In this step we are processing raw data from sequencing technology to obtain high quality data for later processing. Every step at this point is not specific of *de novo* assembly and common to many bio-informatics analysis.

-   Secondary analysis: Secondary analysis refer here the the main type of analysis which is here *de novo* assembly i.e. the obtention the la largest continuous or scaffold sequence representative of the target individual. That includes quality controls.

-   Tertiary Analysis refers to what can be done beyond the resolution of an assembly such as comparative genomics or annotation.

## Objectives

-   Master every steps of *de novo* assembly for eukaryote genomes
-   Interpret the results at every steps
-   Master the use the CLI tools
-   Become fluent with apptainer/docker
-   Be autonomous and independent for debugging

## Requirements

-   Be fluent in Unix/Linux

-   Work on linux or eventually WSL2 on windows

-   Be familiar with the use of apptainer/docker or conda

-   Meets the performance criteria, at least 8 threads & 32GB RAM would be good for starts

## Important notes

### RTFM: Read The F\*\*\* Manual

-   Try `tool -h`, `tool –help`, `tool -help`, or just `tool` or eventually `man tool`. Eventually in combination with `grep`.

-   Try the tool's website <https://www.bioinformatics.babraham.ac.uk/projects/fastqc/>

-   Or maybe the GitHub/GitLab: <https://github.com/s-andrews/FastQC>

-   Look eventually at the paper describing the tool.

### RTFE: Read The F\*\*\* Error \| Top 5

1\. **File Not Found (`FileNotFoundError` or "No such file or directory")**

-   **Example error message:** `bash: ./script.sh: No such file or directory` or `python: FileNotFoundError: [Errno 2] No such file or directory`

-   **Typical cause:** Incorrect path, typo in filename, or missing input files.

2\. **Out of Memory (`OOM_kill` or "Killed")**

-   **Example error message:** `Killed` (on Linux, when a process is stopped by the system's out-of-memory killer), or `MemoryError` (in Python, R).

-   **Typical cause:** Trying to process files or data too large for the available RAM.

3\. **Cannot Find Shared Library (`cannot open shared object file: No such file or directory`, `cannot find xxx.so`)**

-   **Example error message:** `error while loading shared libraries: libXYZ.so: cannot open shared object file: No such file or directory`

-   **Typical cause:** Missing dependencies, or environment (e.g., LD_LIBRARY_PATH) not set correctly after software installation.

-   **hints:** Search for any package that contains this file.

4\. **Permission Denied (`PermissionError` or "Permission denied")**

-   **Example error message:** `bash: ./some_script.sh: Permission denied`, or in Python, `PermissionError: [Errno 13] Permission denied`

-   **Typical cause:** Trying to run or write to a file/folder without the necessary permissions.

5\. **Segmentation Fault (`Segmentation fault (core dumped)`)**

-   **Example error message:** `Segmentation fault (core dumped)`

-   **Typical cause:** Bugs in compiled programs (common in C/C++ binaries used in bioinformatics), or sometimes hardware issues.

-   **hints:** Check for corrupted or incorrect input files and formats.

### STFE: Search The F\*\*\* Error \| Where ?

-   General Search Engine such as DuckDuckGo or Google or Bing

-   GitHub/GitLab issues or Discussions

-   Community chat (Slack, Discord, Matrix) or forums (Reddit r/bioinformatics, Slack Overflow, Biostars)

-   Eventually but EXTRA CAREFULLY: AI assistance & LLMs