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https://github.com/carolindahms/assembly-with-omni-c

Assemblinng a reference genome with PacBio and Omni-C reads

https://github.com/carolindahms/assembly-with-omni-c

Science Score: 13.0%

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Repository

Assemblinng a reference genome with PacBio and Omni-C reads

Basic Info
  • Host: GitHub
  • Owner: carolindahms
  • Default Branch: main
  • Size: 12.7 KB
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  • Watchers: 1
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Created over 1 year ago · Last pushed over 1 year ago
Metadata Files
Readme

README.md

Genome assembly with PacBio and Omni-C reads

  1. Pre-process reads
    • Convert Pacbio Revio bam files to fastq with pbtk
    • Asses read-length distribution in R plots
    • Remove adaptors with bbtools and HiFiAdapterFilt
  2. Count kmers with meryl
  3. Assess genome with Genomescope2.0
  4. Assemble with hifiasm in solo mode
    • run with different -t -s and purging (-l) settings eg -t 15 or 20; -s 0.75, 0.55 or 0.35, -l 1 for light purging
    • run with optimum K (-k)
  5. Evaluate hifiasm results
    • compare multiple assemblies with different filters using bbtools script statswrapper.sh
    • BUSCO with different databases for both primary and alternate haplotigs using different databases (e.g. vertebrata and actinopterygii)
    • assembly stats with gfastats
    • Merqury plots and stats based on kmers
  6. Purge haplotigs using Genomescope stats and minimap2 + evaluate final contig assembly with gfastats

Scaffolding

  1. Preprocess
  2. Map reads separately with bwa mem following steps from Dovetail tutorial
  3. Pairtools to generate bam file + QC
    • Record valid ligation events with pairtools
    • Sort pairsam
    • Mark duplicates
  4. Scaffolding with YaHS + QC + remove contaminants
  5. Omni-C contact maps with JuicerTools

Owner

  • Login: carolindahms
  • Kind: user

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