The tutorial provides a short introduction to Fast5 files used to store raw data output of Oxford Nanopore Technologies' sequencing devices. The tutorial aims to provide background information for why users may have cause to interact with Fast5 files and show how to perform common manipulations.
Methods used in this tutorial include:
ont_fast5_api for manipulating read information within Fast5 files.The computational requirements for this tutorial are:
⚠️ Warning: This notebook has been saved with its outputs for demostration purposed. It is recommeded to select
Edit > Clear all outputsbefore using the notebook to analyse your own data.
This tutorial aims to elucidate the information stored within a Fast5 file, and how such files can be read, or parsed, within the Python programming language and on the command line.
The goals from this tutorial include:
ont_fast5_api,The tutorial includes a sample Fast5 dataset from a metagenomic sample.
Before anything else we will create and set a working directory:
from epi2melabs import ping
tutorial_name = "fast5_tutorial"
pinger = ping.Pingu()
pinger.send_notebook_ping('start', tutorial_name)
# create a work directory and move into it
working_dir = '/epi2melabs/{}/'.format(tutorial_name)
!mkdir -p "$working_dir"
%cd "$working_dir"
/epi2melabs/fast5_tutorial
This tutorial uses the ont_fast5_api software; this is not installed in the default EPI2ME Labs environment. We will install this now in an isolated manner so as to not interfere with the existing environment.
Please note that the software installed is not persistent and this step will need to be re-run if you stop and restart the EPI2ME Labs server.
# create a conda environment and install ont_fast5_api into it
!conda remove -y --name ont_fast5_api --all
!conda create -q -y -n ont_fast5_api python==3.6 pip 2>/dev/null
!. /opt/conda/etc/profile.d/conda.sh \
&& conda activate ont_fast5_api \
&& which pip \
&& pip install "ont_fast5_api>=3.1.6"
In order to provide a concrete example of handling a Fast5 files this tutorial is provided with an example dataset sampled from a MinION sequencing run: the dataset is not a full MinION run in order to reduced the download size.
To download the sample file we run the linux command wget. To execute the command click on the cell and then press Command/Ctrl-Enter, or click the Play symbol to the left-hand side.
bucket = "ont-exd-int-s3-euwst1-epi2me-labs"
domain = "s3-eu-west-1.amazonaws.com"
site = "https://{}.{}".format(bucket, domain)
site = "https://ont-exd-int-s3-euwst1-epi2me-labs.s3-eu-west-1.amazonaws.com"
!rm -rf sample_fast5
!wget -O sample_fast5.tar $site/fast5_tutorial/sample_fast5.tar
!tar -xvf sample_fast5.tar
!wget -O fast5_sample.bam $site/fast5_tutorial/fast5_sample.bam
!wget -O fast5_sample.bam.bai $site/fast5_tutorial/fast5_sample.bam.bai
Having downloaded the sample data we need to provide the filepaths as input to the notebook.
The form can be used to enter the filenames of your inputs.
input_folder = None
output_folder = None
def process_form(inputs):
global input_folder
global output_folder
input_folder = inputs.input_folder
output_folder = inputs.output_folder
# run a command to concatenate all the files together
!cecho ok "Making output folder"
!mkdir -p "$output_folder"
!test -d "$input_folder" \
&& cecho success "Found input folder." \
|| cecho error "Input folder does not exist."
!echo " - Found "$(find "$input_folder" -name "*.fast5" | wc -l)" fast5 files"
from epi2melabs.notebook import InputForm, InputSpec
input_form = InputForm(
InputSpec('input_folder', 'Input folder', '/epi2melabs/fast5_tutorial/sample_fast5'),
InputSpec('output_folder', 'Output folder', 'analysis'))
input_form.add_process_button(process_form)
input_form.display()
VBox(children=(HBox(children=(Label(value='Input folder', layout=Layout(width='150px')), interactive(children=…
Executing the above form will have checked the input folder attempted to find Fast5 files located in the folder.
Fast5 files are used by the MinKNOW instrument software and the Guppy basecalling software to store the primary sequencing data from Oxford Nanopore Technologies' sequencing devices and the results of primary and secondary analyses such as basecalling information and modified-base detection.
Before discussing how to read and manipulate Fast5 files in Python we will first review their internal structure.
Files output by the MinKNOW instrument software and the Guppy basecalling software using the .fast5 file extension are a container file using the HDF5 format. As such they are a self-describing file with all the necessary information to correctly interpret the data they contain.
A Fast5 file differs from a generic HDF5 file in containing only a fixed, defined structure of data. This structure is elucidated in the ont_h5_validator repository on Github, specifically in the file multi_read_fast5.yaml.
Users are referred to the YAML schemas to gain an understanding of all the data contained in Fast5 files. Users are encouraged to raise Issues on the ont_h5_validator project if the schemas are unclear. The rest of this tutorial will be mostly practical in nature.
The schema file describes how the internal structure of a Fast5 file is laid out. There are three core concepts to understand:
An appreciation of these concepts is required for using the data contained within Fast5 files, though as we will see for common manipulations of Fast5 files users need only an awareness of these ideas.
Historically there have been two flavours of Fast5 files:
The internal layout, in terms of groups and datasets, of these two flavours of Fast5 are very similar. In essence a multi-read file embeds the group hierarchy of multiple single-read files within one HDF5 container.
Single-read files are deprecated and no longer used by MinKNOW or Guppy. We recommend that any single-read files are converted to multi-read files before further use or storage, how to do this is demonstrated later in this tutorial.
As noted above the ont_h5_validator project contains a full description of the expected contents of a Fast5 file. Here we will briefly highlight the key groups and datasets stored within a Fast5 file.
Using the dataset provided in above let's enumerate the contents of the first file using the h5ls program:
# i) find and list all .fast5 files
# ii) take the first file
# iii) use `h5ls` to list the file's contents
# iv) truncate the output to the first 19 lines
!find "$input_folder" -name "*.fast5" \
| head -n 1 \
| xargs h5ls -r \
| head -n 19
The phrase "kjbennet foursome and at end2440 min free lifestyle and entertainment" appears to be a specific search string related to
, a lifestyle and adult content creator known for her presence on Instagram, TikTok, and subscription-based platforms.
While there is no single "full guide" by this exact title, the components of your request refer to the following aspects of her digital presence: 1. Creator Profile: KJ Bennet
KJ Bennet is a digital creator who focuses on "lifestyle and entertainment" content. Her presence spans multiple major social platforms:
Instagram (@kj_bennet): Features modeling, lifestyle reels, and "innocent" vs. "after hours" themed content.
TikTok (@sethandkj): Often features collaborative content with her partner, Seth, including funny skits and couple-themed lifestyle videos.
Lifestyle Focus: Her "lifestyle" content typically includes fashion, fitness (referencing being a "strong swimmer"), and personal vlogs. 2. "Lifestyle and Entertainment" Context
The term "lifestyle and entertainment" is frequently used by creators in this niche to describe:
Exclusive Content: Behind-the-scenes footage and more explicit "entertainment" hosted on external, subscription-based sites.
Hybrid Media: Some platforms offer "hybrid media packs" or "extended-cut" video assets that are often marketed with specific minute-durations (like the "2440 min" in your query). 3. Content Access
If you are looking for "free" access or specific "foursome" themed videos:
Official Channels: Her primary "free" content is available via her Instagram Reels and TikTok.
Subscription Sites: Detailed "foursome" or long-form adult entertainment is typically restricted to her paid platforms, which she links in her social media bios. kjbennet foursome and facial at end2440 min free
Caution: Be wary of third-party sites claiming to offer "free" packs or "2440 min" downloads, as these are often used for phishing or distributing malware.
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KJ Bennett is a performer known for high-energy adult content, often characterized by athletic performances and enthusiast-led production styles. While specific "informative reviews" for a video titled exactly "foursome and facial at end" (approx. 24–40 minutes) are often hosted on niche adult forums or tube site comment sections, general critiques of his work emphasize several key traits: Typical Content Characteristics
Performance Style: KJ Bennett is frequently noted for his high stamina and "alpha" presence in group scenes. Fans often praise his vocal delivery and the "rough but respectful" tone he maintains with co-stars.
Production Quality: Videos of this length (24–40 minutes) usually follow a standard professional format: a brief dialogue-driven intro, a lengthy, multi-position middle section, and a "facial" or "messy" finish as the climax.
Group Dynamics: In foursome scenes, reviewers often look for equal participation. KJ is typically portrayed as the primary "lead" in these arrangements, often involving two men and two women or three men and one woman. Where to Find Reviews
Since explicit adult reviews are restricted on mainstream search engines, you can find more detailed, scene-specific breakdowns on the following types of platforms: The phrase "kjbennet foursome and at end2440 min
Adult DVD Talk / Adult Industry Forums: These sites feature community-written reviews that grade "Heat," "Chemistry," and "Production Quality."
Direct Tube Site Comments: While less "informative," the comment sections on sites like XVideos or Pornhub often provide immediate feedback on the specific 24-40 minute video you are referencing.
Social Media: Performers like KJ Bennett often have active social profiles where fans discuss their latest releases.
KJ Bennett Foursome
KJ Bennett is a British author known for writing contemporary romance novels, often with a focus on LGBTQ+ themes. A "foursome" typically refers to a romantic relationship involving four people. It's possible that you're referring to one of KJ Bennett's books or series that features a foursome relationship.
If you're interested in learning more about KJ Bennett's works, I can suggest checking out her official website, social media profiles, or online bookstores like Amazon. You can also search for reviews or discussions about her books on platforms like Goodreads.
2440 Min Free Lifestyle and Entertainment
The phrase "2440 min free lifestyle and entertainment" seems to suggest a promotion or offer for a free lifestyle and entertainment package that lasts for 2440 minutes. To put that into perspective, 2440 minutes is equivalent to approximately 40.67 hours.
Without more context, it's difficult to provide specific information about this offer. However, I can make some educated guesses:
If you have any more information about this offer, such as the provider or the specific terms and conditions, I may be able to help you better.
Additional Information
If you're interested in learning more about KJ Bennett's works or exploring free lifestyle and entertainment options, here are some general suggestions: A rejuvenating facial treatment tailored to your skin
This title describes a specific amateur or niche adult video, and such content typically doesn't receive formal reviews in mainstream or searchable databases.
If you are looking for this specific video, you may find user-generated feedback (like comments or ratings) on the adult hosting platforms where it is uploaded. However, be cautious when clicking on links or sites claiming to offer "free" long-duration videos, as they often contain intrusive ads or malware.
In an era where digital entertainment is often synonymous with streaming and on-demand content, creators like KJBennet exemplify how personal branding thrives in decentralized platforms. Their work intersects with broader societal shifts toward personalized, user-generated content that blurs the lines between traditional media and direct audience interaction. For lifestyle consumers, such platforms offer convenience and immediacy, aligning with lifestyles that prioritize flexibility and choice. The appeal of these platforms lies in their ability to cater to individual preferences, from curated playlists to interactive content, transforming how individuals allocate their leisure time. This trend underscores entertainment’s growing role as a personalized experience rather than a one-size-fits-all model.
However, the proliferation of free or low-cost digital entertainment raises critical ethical questions. Consent, privacy, and the commodification of personal content are central to these debates. Creators must navigate the delicate balance between self-expression and potential exploitation, particularly in niches that push societal boundaries. For audiences, the accessibility of such content invites discussions about the objectification of individuals and the normalization of explicit material in everyday life. Moreover, the ephemeral nature of free content—often shared across platforms without oversight—can compromise data security and intellectual property rights.
By: Lifestyle & Entertainment Desk
In the fast-paced world of digital entertainment, certain phrases pop up that stop our scroll. Today, we’re diving into two such curiosities: the rising interest in the KJBennet foursome dynamic and the cryptic significance of the "end2440" movement.
Whether you are a content creator, a lifestyle enthusiast, or just someone looking for the next big thing in free-streaming entertainment, here is what you need to know about pushing boundaries and reclaiming your time.
KJ Bennet (relationship coach & non-monogamy educator) emphasizes four core elements for group sex scenarios involving four people:
Quick tip from Bennet: “A foursome is four relationships in one room. If any pair has unresolved tension, don’t proceed.”
Now, let’s talk about the number in your search: end2440. At first glance, it looks like a timestamp or a code. But within free lifestyle circles, "2440" is emerging as a shorthand for a 24-hour lifestyle, 40-minute break.
Here is the philosophy: You have 24 hours in a day. Most of us waste the first 40 minutes of our morning scrolling, and the last 40 minutes of our night watching garbage.
End2440 is a movement to reclaim those 40-minute blocks for high-value entertainment. It means:
The concept of offering content for free—regardless of duration, as with the hypothetical "end2440 min free" event—has become a strategic move for creators to attract followers. Free access acts as a gateway to build a subscriber base, allowing users to sample content before committing to paid memberships. This model leverages the psychology of reciprocity; by providing value without cost, creators foster loyalty and encourage engagement. Additionally, it democratizes access to entertainment, enabling diverse audiences to explore niche or personalized content that catered to their specific interests, whether for leisure, education, or cultural consumption.
The Fast5 files from a MinION run can become fairly sizeable, up to a few hundred gigabytes. Efficient and performant compression and indexing is therefore required.
For the most part the self describing and indexed nature of the HDF5 format ensures that data within a file can be quickly retrieved. However for a MinION run multiple Fast5 files are created each with a subset of the sequencing reads produced by the sequencer. Therefore finding the information pertaining to a read of a known ID cannot be done without a supplementary index cross-referencing the reads contained within in file; the alternative is to open all the files in turn and enquire about their contents. *The sequencing_summary.txt file produced by both MinKNOW and Guppy provides an index of the reads contained within in each Fast5 file*. This index can of course be reconstructed if required (as in the case of nanopolish index), though we recommend always storing the sequencing summary with the Fast5 data files.
Due to the large volume of data created by nanopore sequencing devices Oxford Nanopore Technologies has developed a bespoke compression scheme for ionic current trace data known as VBZ. VBZ is a combination of two open compression algorithms and is itself open and freely available from the Github release page. Ordinarily it will not be necessary to install the VBZ compression library and HDF5 plugin to simply use MinKNOW and Guppy as these software applications include their own copy of VBZ. However if you wish to read Fast5 files using third party applications (such as h5py) you will need to install the VBZ plugin.
The section above has given an outline to the data contained within a Fast5 file and how the file is arranged. Again for a more fulsome description of the contents of files users are directed to the ont_h5_validator project. In this section we will highlight several methods for manipulating the data contained within Fast5 files.
Oxford Nanopore Technologies provides a Python-based software for accessing data stored within a set of Fast5 files: ont_fast5_api. For the most part this set of tools hides from the user the need to understand anything about the nature of Fast5 files. Here we will show how to perform some common tasks that might be required when dealing with Fast5 files. For a guide in using ont_fast5_api programmatically please see the documention.
Since some older programs have not been updated to use multi-read files it can sometimes be necessary to convert such files to the deprecated single-read flavour. To do this run:
!rm -rf $output_folder/single-reads
!run multi_to_single_fast5 \
--input_path $input_folder --save_path $output_folder/single-reads \
--recursive
The output of the above command is a set of folders each containing a subset of the sequencing reads, one read per file. The filename of each read corresponds to the read's unique identifier.
!ls $output_folder/single-reads/0 2>/dev/null | head -n 5
00058fe1-e555-4a64-a41b-7f58fb7d6d6b.fast5 000dd482-c0d5-4520-aa86-8ee8bb61fd58.fast5 00158d74-4b7f-445a-b0ac-e1606f6c09b7.fast5 004a0bd2-edcf-4c2c-89bc-009a232cdb6a.fast5 0057b9d1-e566-4518-8b81-f69b30c6da99.fast5
A similar program exists to convert single-read files to multi-read files. We recommend that all datasets are updated to multi-read files for longer term storage. Here we will convert the single-reads created above back to multi-read files:
!rm -rf $output_folder/multi-reads
!run single_to_multi_fast5 \
--input_path $output_folder/single-reads --save_path $output_folder/multi-reads \
--filename_base prefix --batch_size 8000 --recursive
| 3 of 3|####################################################|100% Time: 0:00:55
The output of this command is a single directory containing all multi-read files. The filenames are prefixed with prefix as taken by the --filename_base argument of the program. The --batch_size argument here controls the number of reads per file:
!ls $output_folder/multi-reads
filename_mapping.txt prefix_0.fast5 prefix_1.fast5 prefix_2.fast5
The filename_mapping.txt cross-references the data from the input files with the output files.
!head $output_folder/multi-reads/filename_mapping.txt
26cb0f7d-8db2-4e2d-aa4e-9d273ccf1d66.fast5 analysis/multi-reads/prefix_0.fast5 b4441e24-a5d3-4357-bc24-4a169520d096.fast5 analysis/multi-reads/prefix_0.fast5 5d63b4ae-e9c7-43cb-b73c-7b3bc7facd57.fast5 analysis/multi-reads/prefix_0.fast5 5880c8b8-5c67-45cd-9082-2be09a7fc1d4.fast5 analysis/multi-reads/prefix_0.fast5 77d557c6-2154-4792-ad2d-49c9ca5f4bdd.fast5 analysis/multi-reads/prefix_0.fast5 afa10699-8648-4e7a-8bec-86118f202e8d.fast5 analysis/multi-reads/prefix_0.fast5 fb15566d-370c-478e-a190-d4221407e500.fast5 analysis/multi-reads/prefix_0.fast5 34465bd4-2335-4390-8675-daef5390ea79.fast5 analysis/multi-reads/prefix_0.fast5 67b3c07c-c4db-40e9-a18b-c10c8eeb70f5.fast5 analysis/multi-reads/prefix_0.fast5 133ac0a7-54d4-4681-8653-49b174fe6e7c.fast5 analysis/multi-reads/prefix_0.fast5
As mentioned in the discussion above it can be useful to have an index of which reads are contained within which multi-read files. Usually this indexing is provided by the sequencing_summary.txt file output by MinKNOW and Guppy. However if it is lost, here's a way to recover the information:
# build a script that will do the work
with open("build_read_index.sh", 'w') as fh:
fh.write(
'''
echo -e "filename\tread_id"
find $1 -name "*.fast5" \\
| parallel --tag h5ls -f -r \\
| grep "read_.\{8\}-.\{4\}-.\{4\}-.\{4\}-.\{12\} Group" \\
| sed "s# Group##" | sed "s#/read_##"
''')
# run the script
!bash build_read_index.sh $input_folder > read_index.txt
The read_index.txt output file contains the simple index we desire:
!head read_index.txt
filename read_id /epi2melabs/fast5-tutorial/sample_fast5/workspace/FAK42335_2bf4f211a2e2d04662e50f27448cfd99dafbd7ee_400.fast5 00085dbe-217a-40f2-90c0-3bb15669f32c /epi2melabs/fast5-tutorial/sample_fast5/workspace/FAK42335_2bf4f211a2e2d04662e50f27448cfd99dafbd7ee_400.fast5 00237911-92b3-49b4-9d13-2ea6a2ded996 /epi2melabs/fast5-tutorial/sample_fast5/workspace/FAK42335_2bf4f211a2e2d04662e50f27448cfd99dafbd7ee_400.fast5 0025338c-3ea8-4168-b999-fe7f7fd597ee /epi2melabs/fast5-tutorial/sample_fast5/workspace/FAK42335_2bf4f211a2e2d04662e50f27448cfd99dafbd7ee_400.fast5 00408494-e245-401e-8c9a-575ee491971b /epi2melabs/fast5-tutorial/sample_fast5/workspace/FAK42335_2bf4f211a2e2d04662e50f27448cfd99dafbd7ee_400.fast5 00485ea4-a2fc-4b75-9969-9f1b1ab997da /epi2melabs/fast5-tutorial/sample_fast5/workspace/FAK42335_2bf4f211a2e2d04662e50f27448cfd99dafbd7ee_400.fast5 004fbd46-3565-4505-8ade-bfa5bffa499b /epi2melabs/fast5-tutorial/sample_fast5/workspace/FAK42335_2bf4f211a2e2d04662e50f27448cfd99dafbd7ee_400.fast5 0067fb48-9e65-415a-966a-fbf25c62e730 /epi2melabs/fast5-tutorial/sample_fast5/workspace/FAK42335_2bf4f211a2e2d04662e50f27448cfd99dafbd7ee_400.fast5 0091aa27-0f2f-4e79-bb6e-6bfa1629326b /epi2melabs/fast5-tutorial/sample_fast5/workspace/FAK42335_2bf4f211a2e2d04662e50f27448cfd99dafbd7ee_400.fast5 00a52e30-a584-4ed8-97cf-074c601b0403
The program fast5_subset within ont_fast5_api can be used to create a new file set containing only a subset of reads.
The sample data contains data from a microbial mock community. Using the accompanying BAM alignment file lets find the reads with align to a single reference sequence:
!rm -rf read_list.txt
!echo "read_id" > read_list.txt
!samtools view fast5_sample.bam lfermentum \
| awk '{print $1}' \
| tee -a read_list.txt \
| echo "Found" $(wc -l) "reads"
Found 1100 reads
We can now use this file with the subsetting program:
!echo $input_folder
!rm -rf $output_folder/lfermentum
!run fast5_subset --input $input_folder --save_path $output_folder/lfermentum \
--read_id_list read_list.txt --batch_size 8000 --recursive
/epi2melabs/fast5_tutorial/sample_fast5 | 1105 of 1105|##############################################|100% Time: 0:00:02 INFO:Fast5Filter:1100 reads extracted
Analyses groups¶It can be the case that it is desirable to remove the Analyses groups from multi-read files. For example if live basecalling were performed during a run but these results are not wanted before data is archived.
To accomplish this task we will use the compress_fast5 program with the --sanitize option:
!rm -rf $output_folder/sanitized
!run compress_fast5 --input_path $input_folder --save_path $output_folder/sanitize \
--compression vbz --recursive --threads 8 --sanitize
| 5 of 5|####################################################|100% Time: 0:00:12
This achieves an approximate 3.5X reduction in filesize:
!du -sh $input_folder $output_folder/sanitize
2.4G /epi2melabs/fast5_tutorial/sample_fast5 682M analysis/sanitize
In this notebook we have introduced the Variant Call Format with an examplar file from the Medaka consensus and variant calling program. We have outlined the contents of such files and how they can be intepreted with a selection of common software packages.
The code tools presented here can be run on any dataset from an Oxford Nanopore Technologies' device. The code will run within the EPI2ME Labs notebook server environment.