genomisc-training

Miscellaneous materials (tutorials, exercises, testdata) to develop essential 'survival'-skills in bioinformatics.

git clone..

contact: [email protected]

1. Introduction
2. Reproducible science
3. The command line 1. Basics 2. writing/running scripts
4. Docker
5. Using HPC 1. Connecting 2. Job submission
   1. SLURM
   2. PBS
6. Manipulating FASTQ data
7. FASTQ basics
8. FASTQ file manipulation using command line skills
9. FASTQ trimming 1. Fastx-toolkit 2. Trimmomatic
10. Error correction 1. Illumina data 2. PacBio data
11. paired end read merging 1. FLASh 2. Pear
12. Demultiplexing
13. Read mapping
14. BWA
15. Bowtie
16. RADseq data
17. Stacks
18. Pyrad
19. SNP calling
20. Freebayes
21. SNP annotation
22. SNPeff
23. Genome assembly
24. Illumina data 1. Velvet 2. Spades 3. Celera
25. PacBio 1. CANU 2. FALCON 3. MIRA
26. Hybrid 1. MIRA 2. Spades 3. Celera
27. Metaassembly, Gapfilling and polishing 1. PBjelly 2. quickmerge
28. Assembly evaluation 1. Basic stats 2. Completeness 3. Contamination
29. RNAseq data
30. Denovo
31. Reference genome based
32. metabarcoding
33. A basic BLAST search
34. MEGAN
35. Structural genome annotation
36. Functional genome annotation

Introduction

Manipulating FASTQ data

FASTQ file manipulation using command line skills

The UNIX command line provides highly efficient, simple and incredibly powerful tools for text file manipulation. Much of the NGS data you will be processing are nothing more than text files. Proficiency with some of these basic tools will get you a long way (you may not need anything else), so I have prepared a number of simple exercises that should help you develop your command line skills, specifically in the context of FASTQ data manipulation. It will hopefully also help you to get a feel for the kind of data that you will be working with. Get started here.

Read mapping

RADseq data

SNP calling

SNP annotation

Genome assembly

RNAseq data

metabarcoding