<p>Early MinION sequencing runs had forward and reverse DNA templates joined together by a hairpin adapter, so that the sequencer would read both strands from the same template. The consensus sequence that was generated by combining the base calls of opposite strands is referred to as a 2D read.</p>

<p>Due to <a href="https://nanoporetech.com/about-us/news/oxford-nanopore-announces-favourable-outcome-uk-and-german-patent-litigation-against" rel="nofollow noreferrer">a dispute with Pacific Biosciences</a>, and for other reasons related to chemistry and basecalling, the equivalent mode in current sequencing runs is called 1D². There is no physical ligation of forward and reverse templates, but the kit and flow cell chemistry are modified to encourage the reverse strand to follow the forward strand very soon afterwards through the pore, with the joining and consensus generation carried out in software after the sequencing is done. In the output fast5 files, these 1D² reads can also be referred to as 2D.</p>

CC BY-SA 4.0
2018-11-27T20:38:43.940Z
2019-05-31T14:21:26.080Z
2019-05-31T14:21:26.080Z
gringer
<p>Reading the <a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0997-x" rel="nofollow noreferrer">Mash: fast genome and metagenome distance estimation</a> paper, I see the reference to "2d reads" notion under the <a href="https://nanoporetech.com/products/minion" rel="nofollow noreferrer">minION</a> context (a sequencing technique)<br>
e.g</p>

<pre><code>    In both cases Mash was able to
correctly differentiate these closely related species
(ANI ≈ 95 %) using 43,806 and 91,379 sequences collected
from single MinION R7.3 runs of B. anthracis
Ames and B. cereus ATCC 10987, respectively (combined
1D and 2D reads) &lt;----------  HERE. 
</code></pre>

<p>But couldn't find any reference in Wikipedia or online papers to what it is<br>Can someone shed some light?</p>

CC BY-SA 4.0
2018-11-27T19:06:23.047Z
see here: https://www.biostars.org/p/176781/
Peter Menzel
<phylogenetics><genome-sequencing>
What are 2D reads in the Oxford MinIon?
# What are 2D reads in the Oxford MinIon?

(Asked by: username_0 on 2018-11-27)

Reading the Mash: fast genome and metagenome distance estimation paper, I see the reference to "2d reads" notion under the minION context (a sequencing technique)
e.g
    In both cases Mash was able to
correctly differentiate these closely related species
(ANI ≈ 95 %) using 43,806 and 91,379 sequences collected
from single MinION R7.3 runs of B. anthracis
Ames and B. cereus ATCC 10987, respectively (combined
1D and 2D reads) <----------  HERE. 

But couldn't find any reference in Wikipedia or online papers to what it isCan someone shed some light?

**Tags:** phylogenetics, genome-sequencing
> **Comments:**
> **username_1**: see here: https://www.biostars.org/p/176781/  

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## 1 answers

### Answer by username_2 on 2018-11-27. Score: 5 | Accepted answer

Early MinION sequencing runs had forward and reverse DNA templates joined together by a hairpin adapter, so that the sequencer would read both strands from the same template. The consensus sequence that was generated by combining the base calls of opposite strands is referred to as a 2D read.

Due to [a dispute with Pacific Biosciences](https://nanoporetech.com/about-us/news/oxford-nanopore-announces-favourable-outcome-uk-and-german-patent-litigation-against), and for other reasons related to chemistry and basecalling, the equivalent mode in current sequencing runs is called 1D². There is no physical ligation of forward and reverse templates, but the kit and flow cell chemistry are modified to encourage the reverse strand to follow the forward strand very soon afterwards through the pore, with the joining and consensus generation carried out in software after the sequencing is done. In the output fast5 files, these 1D² reads can also be referred to as 2D.


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