SPART

SPART, a Semi-automated pipeline for assembling reference sequence of telomere-to-telomere (T2T).

Quick install and start

• Install
• Dependencies
• Running pipeline with snakemake
  • Output files

Run step by step

• 00_Contig screen
  • Fastp :was used to filter adapter sequences, primers and other low quality sequence from raw sequencing reads.
  • Hifiasm
  • Verkko
  • Flye
  • Remove MT & CP
• 01_Contig scaffolding
  • Bionano
  • Hi-C
• 02_Gap patching
  • Manual operation
  • telomere patching
  • Centromeric region analysis
• 03_Polishing
• 04_Evaluation
  • BUSCO
  • mapping rates & coverages
  • LTR
  • QV
  • BACs