TE_pangenome

Transposon-focus pangenome pipeline for polymorphic transposable elements in diverse populations

Background

Using GraffiTE for inspiration/model, this pipeline extends usage for >5 samples. The current usage is 60 samples

Programs used:

• fasterqdump v3.0.0 (https://github.com/ncbi/sra-tools/wiki/HowTo:-fasterq-dump)
• minimap2 v2.17-r941 (https://github.com/lh3/minimap2)
• samtools v1.16.1 (https://github.com/samtools/samtools/releases/)
  • htslib v1.16
• sniffles v2.4 (https://github.com/fritzsedlazeck/Sniffles)
  • python v3.10.8 (https://www.python.org/downloads/release/python-3108/)
• NanoPlot v1.39.0 (optional) (https://github.com/wdecoster/NanoPlot)
  • python v3.10.8
• RepeatMasker v4.1.0 (https://www.repeatmasker.org/RepeatMasker/)
• bcftools v1.8 (https://github.com/samtools/bcftools/releases/)
• vg v1.65.0 (https://github.com/vgteam/vg/releases)

Steps

1. Sample preparation

2. Sample alignment

3. QC - Quality reads (Optional)

4. Mask TEs

5. Filtration

6. Genotyping

7. Analysis

7a.

7b.