Skip to content

Added software sources #2

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
Easybel merged 1 commit into from
May 6, 2023
Merged

Added software sources #2

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
16 changes: 13 additions & 3 deletions 0_WGSPipeline/README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,11 +1,21 @@
# About the scripts in this folder:

- **0_DicIndex.sh**
- The dictionaries needed for the alignment steps are indexed and sorted.
- The dictionaries needed for the alignment steps are indexed and sorted.
- Programs used in the script
- BWA https://github.com/lh3/bwa
- samfold from https://github.com/samtools/samtools
- Picard https://github.com/broadinstitute/picard (requires Java)

- **1_QCScript.sh**
- Raw reads are trimmed and adapters are removed. The read quality is assessed before and after the trimming.
- Programs used in the script
- FastQC https://www.bioinformatics.babraham.ac.uk/projects/download.html#fastqc
- Trimmomatic https://github.com/usadellab/Trimmomatic

- **2_CombiScriptSamtools.sh**
- The trimmed reads are aligned to the reference and variants are called. The coverage at each position is evaluated.

- The trimmed reads are aligned to the reference and variants are called. The coverage at each position is evaluated.
- Programs used in the script
- bwa and samtools, see above
- BCFtools https://github.com/samtools/bcftools
- Bedtools 2 https://github.com/arq5x/bedtools2