Adding two new presentations #57
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bebatut
reviewed
Dec 5, 2019
_materials/1_introduction.html
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| ### Schedule |
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I would not put the schedule here (but in the handbook), because we could use the slides not only for a 2-days workshop and also we are not sure about the timing
| ### Data analysis | ||
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| <img src="/images/materials/bioinformatics/3.svg" width="400"> |
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This image is not really true. Most of the time we do not have the reference genome of the bacteria, so we look for the closest relatives. And we do not really care where it maps on the reference.
What we are more interesting is to identify a taxonomic assignation for the reads
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| layout: slides | |||
| title: "What is Nanopore-Sequencing?" | |||
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| title: "What is Nanopore-Sequencing?" | |
| title: "What is Nanopore Sequencing?" |
| ### How to Read DNA | ||
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| [Video](https://nanoporetech.com/applications/dna-nanopore-sequencing) |
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| [Video](https://nanoporetech.com/applications/dna-nanopore-sequencing) | |
| <iframe src="https://player.vimeo.com/video/337258910" width="640" height="360" frameborder="0" allow="autoplay; fullscreen" allowfullscreen></iframe> | |
| <p><a href="https://vimeo.com/337258910">Animation: Nanopore sequencing</a> from <a href="https://vimeo.com/user5318092">Oxford Nanopore</a> on <a href="https://vimeo.com">Vimeo</a>.</p> |
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| layout: slides | |||
| title: "Further Imformation about Nanopore-Sequencing" | |||
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| title: "Further Imformation about Nanopore-Sequencing" | |
| title: "Further Information about Nanopore Sequencing" |
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| - **Fragmentation Mix (FRA):** Ligases (Exonucleases) to cut DNA into shorter pieces. Will cut at certain sequences. | ||
| - **Rapid Sequencing Adapter (RAP):** Ligation of adapters to the DNA fragments (leader and hairpin adapter). The leader adapter will allow the DNA to dock to the nanopore. The hairpin adapter is then for the complement strand. | ||
| - **Flush Tether (FLT):** Guides the motorprotein to the pores. |
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| - **Flush Tether (FLT):** Guides the motorprotein to the pores. | |
| - **Flush Tether (FLT)** to guide the motorprotein to the pores |
| - **Fragmentation Mix (FRA):** Ligases (Exonucleases) to cut DNA into shorter pieces. Will cut at certain sequences. | ||
| - **Rapid Sequencing Adapter (RAP):** Ligation of adapters to the DNA fragments (leader and hairpin adapter). The leader adapter will allow the DNA to dock to the nanopore. The hairpin adapter is then for the complement strand. | ||
| - **Flush Tether (FLT):** Guides the motorprotein to the pores. | ||
| - **Seqeuncing Buffer (SQB):** For the ionic current. |
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| - **Seqeuncing Buffer (SQB):** For the ionic current. | |
| - **Sequencing Buffer (SQB)** to conduct the ionic current |
| - **Rapid Sequencing Adapter (RAP):** Ligation of adapters to the DNA fragments (leader and hairpin adapter). The leader adapter will allow the DNA to dock to the nanopore. The hairpin adapter is then for the complement strand. | ||
| - **Flush Tether (FLT):** Guides the motorprotein to the pores. | ||
| - **Seqeuncing Buffer (SQB):** For the ionic current. | ||
| - **Flush Buffer (FB):** For washing. |
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| - **Flush Buffer (FB):** For washing. | |
| - **Flush Buffer (FB)** to wash |
| - **Flush Tether (FLT):** Guides the motorprotein to the pores. | ||
| - **Seqeuncing Buffer (SQB):** For the ionic current. | ||
| - **Flush Buffer (FB):** For washing. | ||
| - **Loading Beads (LB):** To increase the molecular weight of the DNA. Helps to suck the DNA from the loading port into the flowcell. |
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| - **Loading Beads (LB):** To increase the molecular weight of the DNA. Helps to suck the DNA from the loading port into the flowcell. | |
| - **Loading Beads (LB)** to increase the molecular weight of the DNA | |
| It helps to suck the DNA from the loading port into the flowcell |
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As the content here is mostly text, not slides, we could maybe move it to the Sequencing protocol as a comment for the teachers
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I did the changes. PR can be merged if there is furhter requests. |
mmiladi
reviewed
Oct 8, 2020
| - The quality of the reads decreases at the end of a read like in Illumina Sequencing. | ||
| - Average length 2-10 kb reads. Error Rate 15-40%. | ||
| - The quality of the reads not decreases at the end of a read like in Illumina Sequencing. | ||
| - Average length 2-10 kb reads. Error Rate 15-40% (which comes mostly from the basecalling). |
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Error rate is <10% nowadays, ~5-6%.
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Thanks much @heylf . I added a single comment. |
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Bioinfroamtics presentation and Nanopore Sequencing presentation