HackBio-Genomics-Workshop

Find all the tasks related to the training!

STAGE ZERO

• Used BASH to carry out basic and introductory tasks

STAGE ONE

• Worked with simple biological datasets
• Softwares used:

1. fastqc (quality control)
2. multiQC (assembling quality control reports)
3. fastp (trimming sequence adapters)
4. fastx (fastq_to_fasta : convert fastq to fasta)
5. bwa (assembling genomes)
6. samtools (manipulating sam/bam/cram files)

Note: All the results are stored in output file and the sample datasets are in the raw_reads file

STAGE TWO

• Followed the tutorial from:

1. https://github.com/Fredrick-Kakembo/Somatic-and-Germline-variant-Identification-from-Tumor-and-normal-Sample-Pairs/blob/main/README.md
2. https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/somatic-variants/tutorial.html

• Prepared a summary report of the task