NGS exercise
Welcome to the NGS exercise.
Here, you will try to run a pipeline for analysis of SARS-CoV-2 sequences in wastewater.
If you are not familiar with running bioinformatic tools in the command line, please go to the folder "For those not doing the NGS exercise" instead.
Happy learning!
- extra_materialsextra_materials
- solutions_and_output_filessolutions_and_output_files
- intermediate_filesintermediate_files
- Sample1_depths.txtSample1_depths.txt
- Sample1_hostmapped_trimmed.samSample1_hostmapped_trimmed.sam
- Sample1_R1_val_1.fq.gzSample1_R1_val_1.fq.gz
- Sample1_R2_val_2.fq.gzSample1_R2_val_2.fq.gz
- Sample1_rmhost_trimmed.fq.gzSample1_rmhost_trimmed.fq.gz
- Sample1_sorted_primertrimmed_Wuhanmapping_rmhost_trimmed.bamSample1_sorted_primertrimmed_Wuhanmapping_rmhost_trimmed.bam
- Sample1_sorted_primertrimmed_Wuhanmapping_rmhost_trimmed.bam.baiSample1_sorted_primertrimmed_Wuhanmapping_rmhost_trimmed.bam.bai
- Sample1_sorted_Wuhanmapped_rmhost_trimmed.bamSample1_sorted_Wuhanmapped_rmhost_trimmed.bam
- Sample1_sorted_Wuhanmapped_rmhost_trimmed.bam.baiSample1_sorted_Wuhanmapped_rmhost_trimmed.bam.bai
- Sample1_sorted_Wuhanmapping_rmhost_trimmed.bamSample1_sorted_Wuhanmapping_rmhost_trimmed.bam
- Sample1_sorted_Wuhanmapping_rmhost_trimmed.bam.baiSample1_sorted_Wuhanmapping_rmhost_trimmed.bam.bai
- Sample1_variants.tsvSample1_variants.tsv
- Sample1_lineages.txtSample1_lineages.txt
- Sample1_R1_fastqc.htmlSample1_R1_fastqc.html
- Sample1_R1_val_1_fastqc.htmlSample1_R1_val_1_fastqc.html
- Sample1_R1.fq.gz_trimming_report.txtSample1_R1.fq.gz_trimming_report.txt
- Sample1_R2_fastqc.htmlSample1_R2_fastqc.html
- Sample1_R2.fq.gz_trimming_report.txtSample1_R2.fq.gz_trimming_report.txt
- Sample1_rmhost_trimmed_fastqc.htmlSample1_rmhost_trimmed_fastqc.html
- Sample1_sorted_Wuhanmapped_rmhost_trimmed.bamSample1_sorted_Wuhanmapped_rmhost_trimmed.bam
- Sample2_lineages.txtSample2_lineages.txt
- Sample3_lineages.txtSample3_lineages.txt
- Suggested_solutions.docxSuggested_solutions.docx
- Exercise on WW analysis.docxExercise on WW analysis.docx
- Sample1_R1.fq.gzSample1_R1.fq.gz
- Sample1_R2.fq.gzSample1_R2.fq.gz
- SARS-CoV-2_v5.3.2.primer.bedSARS-CoV-2_v5.3.2.primer.bed
- Wuhan_Hu1.fastaWuhan_Hu1.fasta