Table of Contents

Purpose & Strategy

Our goal here is to analyze the sequencing data from our first barcoded tagmentation plasmid library made in First time: fragment genomes (public copy) .

Computational analysis

Both libraries were prepped using the c.00185.pTwist_BsT-mStayGold_barcode-GG plasmid backbone and tagmented c.00165.Helongata.1H9 gDNA.

Submitted sequencing

| Sample | Plasmid backbone | Sanger (short reads) | Nanopore data Whole Plasmid | Raw reads (.fastq) | NGS | Expected Transformants | Stock Number | | --- | --- | --- | --- | --- | --- | --- | --- | | m.C.00146 | c.00185.pTwist_BsT-mStayGold_Barcode-GG | Dropbox | Dropbox | Dropbox | Dropbox | 5.9 million | s.Ec.C.00349 | | m.C.00147 | c.00185.pTwist_BsT-mStayGold_Barcode-GG | Dropbox | Dropbox | Dropbox | Dropbox | 8.7 million | s.Ec.C.00350 |

NOTE: If @m.C.00146 does not look good, you may want to redo the miniprep by re-culturing it from the glycerol stock @s.Ec.C.00349 because I messed up on the miniprep.

In progress:

• Pick ~8 colonies of transformation number 1 aka F1 and transformation number 2 aka H1 from the 1/1000 or 1/100,000 dilution plate (also in 4C), culture, miniprep, and send for whole plasmid sequencing through Plasmidsaurus.
• NGS:
  • Sample 9: Miniprep of m.C.00146
  • Sample 10: Glycerol stock of m.C.00146
  • Sample 11: Miniprep of m.C.00147
  • Sample 12: Glycerol stock of m.C.00147

Target graphs

Can we have graphs like this!? Genome coverage, insert size distribution etc

Initial analysis

The first thing I did was to take a quick look at the nanopore reads aligned to the plasmid (c-00186). Quick analysis using https://plalign.streamlit.app/