DNA assembly - linnasp/GenomeAnalysis_VT2026_Lab GitHub Wiki

Results from Flye assembly:

• Total length: 16823629
• Fragments: 43
• Fragments N50: 2073827
• Largest frg: 5054216
• Scaffolds: 0
• Mean coverage: 578

Reuslts from BWA + SAMtools (flagstat)

• Total reads: 41585752 + 0 in total (QC-passed reads + QC-failed reads)
• Mapped reads: 99.52%
• Properly paired reads: 98.02%
• Singletons: 0.08%
• 422003 + 0 with mate mapped to a different chr, 422003/41585752*100 = 1.01478%

Results from Pilon:

• Mean frags coverage: 303
• Mean total coverage: 303
• grep -c ">" /home/linnasp/GenomeAnalysis_VT2026_Lab/results/02_assembly/04_Pilon/pilon.fasta 43 Visulized with Bandage: