<p>Albacore can be used to create a fastq, directly from your fast5 files. As such there is no more reason to use poretools, expect perhaps for getting some metadata. With regards to metadata I would like to add that the sequencing_summary.txt generated by albacore also contains a lot of metadata.</p>

CC BY-SA 3.0
2017-12-05T10:30:27.887Z
2017-12-05T10:30:27.887Z
Wouter De Coster
<p>No, poretools does not do basecalling. The <code>poretools fastq</code> command can be used to extract the FASTQ information from the basecalled FAST5 file (via MinKNOW live-basecalling or albacore). Alternatively, both of these basecallers can export a FASTQ file directly if desired.</p>

<p>The difference between a basecalled FAST5 and a nonbasecalled FAST5 is the presence of the FASTQ within the file. This can be directly viewed using an HDF5 viewer, like <a href="https://support.hdfgroup.org/HDF5/doc/RM/Tools.html" rel="nofollow noreferrer">h5dump</a> from the commandline, or <a href="https://support.hdfgroup.org/products/java/hdfview/" rel="nofollow noreferrer">HDFView</a> from the GUI.</p>

CC BY-SA 3.0
2017-12-02T02:56:40.563Z
2017-12-02T03:01:42.357Z
2017-12-02T03:01:42.357Z
Scot
<p>I run the MinION MinKNOW without the live base-calling option. We know there is Metrichor and Albacore to perform base-calling after this process. However, I have not done any base-calling yet.  </p>

<p>My question is: Is it possible to use directly the <code>fast5</code> files with <code>poretools</code> to extract a fastq file without doing any previous base-calling process? I tried it and I get an empty fastq file. </p>

<p>My <code>reads</code> directory only contains the <code>fast5</code> folder and I run: </p>

<p><code>poretools fastq fast5/ &gt; output.fastq</code></p>

<p>Any ideas why do I get an empty file? What is the difference between base-called <code>fast5</code> and non-base-called <code>fast5</code> files? </p>

<p>Now I am trying to do base-calling with Albacore to see if I get a fastq file. </p>

CC BY-SA 3.0
2017-12-05T04:54:04.960Z
You’ve edited the title - I should add that poretools can work with non base-called FAST5 files with some of its options, but not the fastq option. Some of the metadata options will function.
Scot
<minion><albacore>
Can we use non base-called fast5 files in poretools?
# Can we use non base-called fast5 files in poretools?

(Asked by: username_0 on 2017-12-01)

I run the MinION MinKNOW without the live base-calling option. We know there is Metrichor and Albacore to perform base-calling after this process. However, I have not done any base-calling yet.

My question is: Is it possible to use directly the `fast5` files with `poretools` to extract a fastq file without doing any previous base-calling process? I tried it and I get an empty fastq file.

My `reads` directory only contains the `fast5` folder and I run:

`poretools fastq fast5/ > output.fastq`

Any ideas why do I get an empty file? What is the difference between base-called `fast5` and non-base-called `fast5` files?

Now I am trying to do base-calling with Albacore to see if I get a fastq file.

**Tags:** minion, albacore
> **Comments:**
> **username_1**: You’ve edited the title - I should add that poretools can work with non base-called FAST5 files with some of its options, but not the fastq option. Some of the metadata options will function.  

---

## 2 answers

### Answer by username_1 on 2017-12-02. Score: 4 | Accepted answer

No, poretools does not do basecalling. The `poretools fastq` command can be used to extract the FASTQ information from the basecalled FAST5 file (via MinKNOW live-basecalling or albacore). Alternatively, both of these basecallers can export a FASTQ file directly if desired.

The difference between a basecalled FAST5 and a nonbasecalled FAST5 is the presence of the FASTQ within the file. This can be directly viewed using an HDF5 viewer, like [h5dump](https://support.hdfgroup.org/HDF5/doc/RM/Tools.html) from the commandline, or [HDFView](https://support.hdfgroup.org/products/java/hdfview/) from the GUI.


---

### Answer by username_2 on 2017-12-05. Score: 1

Albacore can be used to create a fastq, directly from your fast5 files. As such there is no more reason to use poretools, expect perhaps for getting some metadata. With regards to metadata I would like to add that the sequencing\_summary.txt generated by albacore also contains a lot of metadata.


---

