Find Micronbrane mNGS webinars, whitepapers, protocols, application notes, and product resources for host depletion, library prep, contamination control, pathogen detection, and PaRTI-Seq analysis.
PaRTI-Seq stands for Pathogen Real-Time Identification by Sequencing. It is our mNGS assay for pathogen identification, infectious disease, microbiome, transplant research and other applications consisting of three elements:
PaRTI-Seq can detect all microorganisms such as bacteria, fungi, viruses, and parasites in a sample.
Depending on a host cell’s status within its life cycle, PaRTI-Seq may be able to detect nucleic acids belonging to intracellular viruses and bacteria. However, confirming this would require further testing since the Devin Host Depletion filter captures nucleated host cells infected by intracellular microorganisms. As such, we are continuing analytical and clinical validation experiments to confirm that our filters can enrich cells infected with microorganisms. If you would like to start a collaborative project to test this, we invite you to join our Research Program.
Currently our Microbial Enrichment kit and downstream mNGS library kit detect only DNA viruses. Nonetheless, we are currently developing a separate workflow to detect RNA viruses. Join our newsletter and be notified the moment we launch the assay.
PaRTI-Seq is sequencer agnostic, however, our NGS library kit is currently only compatible with Illumina sequencers but we are quickly developing kits compatible with other sequencing platforms on the market.
Yes, PaRTI-Seq kits are available for both manual and automated protocols. Click here to learn how to integrate PaRTI-Seq into your mNGS workflows HERE.
Currently, the PaRTI-Seq workflow is for Research Use Only (RUO).
The Devin filter is used to remove nucleated cells from biological fluids. It is the only host depletion method that uses a zwitterionic membrane to selectively capture host nucleated cells, increasing the relative proportion of microbial pathogens.
The Devin filter leverages patented Zwitterionic Interface Ultra Self-assemble Coating (ZISC) technology to deplete host nucleated cells. ZISC technology forms a polymer cross-linked layer on the membrane with alternating positive and negative ionic patterns, creating a tightly bound hydration layer. The ionic interactions specifically target the hydrophilic proteins of host cells, retaining them within the filter, while allowing bacteria, viruses, fungi, and parasites to pass through unaltered.
No, it does not. The filter has a pore size of 15–20 μm, which is large enough to allow human cells and larger microorganisms, such as fungi, to pass through. Host cell depletion occurs due to the ionic technology rather than the pore size.
The Devin filter is compatible with all biological fluids.
The filter can be used with sample volumes ranging from 50 μl to 10 ml. To see an example of how Devin and PaRTI-Seq can work with low volumes read our App Note.
The filter has a pore size of 15-20 µm and a diameter of 25 mm. The outer shell is made of polypropylene, and the filter material is a hydrophilic, non-woven fabric.
For whole blood, place the sample in an EDTA tube. For swab samples, immerse the swab in 2-3 ml sterile phosphate-buffered solution (PBS) and stir for 10-15x. If the sample volume is less than 2 ml, top it up with PBS to 2 ml.
We currently recommend using the Devin filter for fresh samples (immediately after collection with storage NOT exceeding 6 hours at ambient temperature or 12 hours at 2-6°C). However, we are testing our products with frozen samples and we have some data on select types. If you plan to use frozen samples, please consult with us so we can share the data and make the best recommendation.
We generally recommend that clinical specimens be processed as soon as possible. When processed immediately, our Devin filter and PaRTI-Seq assay are compatible with any lab’s existing sample-batching policies for PCR and NGS-based assays . If you require your samples to be stored at any point, our kits allow for the following stopping points:
For Devin filter setup, sample-volume guidance, and workflow details, see the Devin Host Depletion Filter page. A written protocol is also available here.
Filter at a slow rate of approximately 1 ml/seconds.
Attach a sterile syringe to the female inlet side of the Devin filter. The inlet is wider and clear with grooves. The outlet is a male luer-lock (white).
Use only sterile syringes, tubes, and tips.
Dispose of the filter in accordance with local rules and regulations for hazardous materials.
No, the filter is disposable and cannot be re-sterilized or reused, including autoclaving or UV treatment.
Store unused filters in a dry place at room temperature (15–30°C).
The shelf life is 3 years.
Do not use filters past their expiration date, which is marked on both the packaging label and the filter container lid as “year-month.” These dates apply only to unopened filters. The lot number is located next to “LOT”. Use the filters promptly once opened.
Always wear appropriate protective equipment, such as masks and disposable gloves. Treat clinical samples as potentially infectious, especially those collected from at-risk patients. These samples should be labeled and handled under safe conditions. Use only sterile syringes, tubes, and tips to prevent nuclease contamination.
Before starting and after completion, spray the laboratory work area with Micronbrane Medical’s XNA Decontaminating Spray Cleaner or equivalent, then wipe with a lint-free cloth. This solution rapidly degrades nucleic acids and inactivates DNases, RNases, and surface enzymes.
For questions or concerns, email support@micronbrane.com.
The Devin Microbial DNA Enrichment Kit is for the extraction and purification of microbial genomic DNA from biological samples for analysis by Next-Generation Sequencing (NGS) or real-time PCR.
The kit includes: Devin Host Depletion filters, a pre-filled plate, elution buffer, incubation buffer, proteinase K, and lysozyme. The pre-filled plate contains: washing buffer 1A, washing buffer 1B, magnetic beads, washing buffer 2A, and washing buffer 2B.
All kit components, except lysozyme and proteinase K, can be stored at room temperature (15-30°C) until the expiration date. Lysozyme should be stored at -20°C upon arrival, although it is transported at room temperature. Proteinase K is stable at room temperature for short-term use but should be stored at -20°C for long-term storage.
You will need: high speed centrifuges, various sizes of tips and pipettes, syringes, Falcon tubes, disposable gloves, 95-100% ethanol, a vortex shaker, DNA low-binding tubes, a magnetic rack for 1.5 ml tubes, a thermomixer, and refrigerators at 4°C and -20°C.
Add 160 μl of elution buffer to the tube containing lysozyme to resuspend it.
After the final wash steps, open the cap of the [MB] tube and heat it at 45°C for up to 10 minutes to dry the magnetic beads. Do not exceed 10 minutes even if the pellet still looks slightly wet.
Add 50 μl of elution buffer to the [MB] tube, shake at 45°C for 5 minutes in a thermomixer, or gently pipette 5 times per minute for 5 minutes. Transfer the supernatant to a new DNA low binding tube.
Always wear appropriate protective equipment such as masks and disposable gloves. Treat clinical samples as potentially infectious. Avoid contact with reagents, and if contact occurs, flush with water immediately. Do not use bleach as the reagent contains guanidine salt.
Before starting and after completion, spray the laboratory work area with Micronbrane Medical’s XNA Decontaminating Spray Cleaner or equivalent, then wipe with a lint-free cloth.
Avoid vigorous shaking to prevent excessive foam. Avoid exposing opened reagents or plates to air. If reagents are colored, replace with a fresh plate. If the temperature is below 20°C, preheat the reagent-filled 96-well plate in an oven (42-60°C) for 5-10 minutes without removing the aluminum foil.
Dispose of all materials in accordance with local rules and regulations for hazardous materials.
Check that you have all the components, and if something is missing, contact support@micronbrane.com immediately and do not proceed with your project.
A system control is highly recommended. We recommend adding a spike-in control, such as ZymoBIOMICS™ Spike-in Control I, with known organisms to a no-template control reaction. We also recommend including a spike-in control in every reaction.
Reagents are all colorless and transparent, except for the magnetic beads. Colored reagents indicate contamination. Replace with a fresh plate before proceeding.
For questions or concerns, email support@micronbrane.com.
The Unison Ultralow DNA NGS Library Preparation Kit is used for generating libraries from very low DNA input. It is part of Micronbrane Medical’s Pathogen Real-Time Identification by Sequencing (PaRTI-Seq) Metagenomic Next-Generation Sequencing (mNGS) assay.
The kit is designed to prepare DNA libraries for sequencing on Illumina platforms, and it can be used for applications including whole genome sequencing, targeted sequencing by capture, and mNGS.
Depending on the kit type, components may include: Transposase Mix, 5x Reaction Buffer, 5x Stop Buffer, Amplification Mix, Index primer, and Purification beads. Some kits also include 2 sets of 24-well plates.
Store the purification beads at 4°C, and store all other reagents at -20°C. Do not use after the expiration date indicated on the outer packaging.
You will need disposable gloves, a disposable mask, pipettes and compatible pipette tips, a vortex, a microcentrifuge, absolute ethanol, nuclease-free water, a PCR thermal cycler, 1.5 ml microcentrifuge tubes, 1.5 ml DNA low binding tubes, 0.6 ml microcentrifuge tubes, a magnetic stand, a Qubit™ dsDNA High Sensitivity Assay Kit, and 0.2 ml PCR tubes.
The recommended input DNA is 1~5 ng or as low as 10 pg in a maximum volume of 8.6 μl for each reaction.
If you have difficulties, consider reducing the DNA input to 2 μl to mitigate potential PCR interference.
Quantify the extracted DNA using a Qubit dsDNA High Sensitivity Assay Kit or other fluorescence-based methods. Nanodrop and other absorbance-based DNA quantitation methods are not recommended.
Thaw the Transposase Mix, 5x Reaction Buffer, and 5x Stop Buffer at room temperature. Thaw the purification beads at room temperature for at least 30 minutes. Thaw the Amplification Mix and index primers on ice. Briefly vortex and spin down all the reagents before use.
Set up the reaction mix on ice, mix well by pipetting (do not vortex), and run the reaction in a thermal cycler according to the conditions in Table 2.
Add 5x Stop Buffer to the reaction, mix well, and put the tube back into the thermal cycler as shown in Table 3.
The number of cycles can be adjusted based on DNA input, refer to Table 6 .
Use Table 7 to calculate the volumes for beads 1 (V1) and beads 2 (V2), which depend on the target library size.
Add V1 of purification beads, mix, and incubate. Collect the supernatant. Add V2 of purification beads, mix, and incubate. Discard the supernatant. Wash the beads twice with 80% ethanol and let them air dry. Elute the DNA with nuclease-free water.
The constructed DNA library can be stored at -20°C.
If the final library is below the detection limit of Qubit, it may still be possible to sequence the library on the Illumina sequencing platform.
Clinical samples may be potentially infectious. Wear a mask, disposable gloves, and protective clothing. Avoid contact with eyes, skin, and clothing. If contact occurs, immediately flush the affected area with water. Use sterile, molecular biology-grade nuclease-free consumables to prevent sample degradation and contamination.
Dispose of all materials in accordance with local rules and regulations for hazardous materials.
For questions or concerns, email support@micronbrane.com.
It is a tool developed by Micronbrane Medical to analyze metagenomic Next-Generation Sequencing (mNGS) data, specifically using the PaRTI-Seq assay. This tool is designed to streamline the analysis of metagenomic data without requiring programming knowledge or special computers.
The user guide is found here.
We use FASTP for QA/QC, BWA MEM for aligning short reads, and Minimap2 for aligning long reads.
We leverage Amazon Web Services cloud computing and Nextflow pipelines to analyze samples quickly and scale with demand.
There is a single database containing over 1,500 pathogens. It’s currently not possible to run an analysis on a subset of this data.
The RUO database is updated on a yearly basis.
Data transfer and analysis are done through Micronbrane Medical’s web services hosted by AWS in Singapore.
You can use any computer with an internet connection to upload sample data and get results.
You need to create an account at the provided website, verify your account via email, and then you can access your project dashboard to begin your analyses. The website is: https://micronbrane.basepairtech.com/.
The RUO version is complementary, but you may need to contact support to get analysis codes.
Contact support@micronbrane.com, and they will email you another code.
Yes, you need to use the PaRTI-Seq Analysis code that came with your kit or was emailed to you. You can create an account without it, but you’ll need to add it later to run analyses.
Go to the drop-down menu in the top right corner, select “Billing and Coupons”, then the “Coupons” tab. Click “Activate coupon” and enter the code.
On the home page, click on “Sign up” and complete the form. You’ll need a password with at least one uppercase letter, one number, and one special character, between 12-16 characters long.
After registering, you will receive a verification email. Click the link in the email.
After verifying your account, click on the Micronbrane Medical logo.
Click on the yellow “Create new project” button or rename Project 1 on the dashboard.
Yes, you can add or remove samples from a project and have multiple analyses within the same project
You can upload samples by clicking “Add samples” in the center of your project screen, or via the “Upload” button, or “Add samples” in the Samples drop down menu.
Samples can be uploaded directly from your computer to the web app. You can also import samples from NCBI/GEO/SRA, BaseSpace, or an FTP/SFTP server.
Make sure that the sample IDs in your sample sheets are unique.
The web app accepts FASTQ and FASTA, either uncompressed or gzip compressed. Here is a detailed list of what the file extensions of those file types can look like: .fastq.gzip, .fq.gzip, .fastq.gz, .fq.gz, .fastq, .fq, .fasta.gzip, .fa.gzip, .fasta.gz, .fa.gz, .fasta, .fa.
It is recommended to leave “Sample Grouping” on automatic. You can also change the sample name. Make sure you select the correct project, platform, data type (PaRTI-Seq), and pipeline (SR-PaRTI-Seq or LR-PaRTI-Seq).
Click on the “Analyses” dropdown menu and select “New analysis” or “Start New Analysis” on the page
You can choose between long-read (LR-PaRTI-Seq) or short-read (SR-PaRTI-Seq) pipelines.
It’s best to use the short reads analysis for samples containing read lengths that are closer to 150 bp in length. Otherwise, the long reads analysis will be more appropriate.
Click the “Add samples” button, select your desired samples, and click “OK”.
Enter a suitable analysis name and then click on the “Run analysis” button.
A sample can take up to a half an hour to analyze. It can take up to 12 hours to process 24 samples in a single run.
The web app can process 24 samples per run and many runs can be started and run simultaneously.
Click on “Analyses,” then “View all analyses,” and select the specific analysis. In the “Input/Output” tab, click on “report.zip” to download the data.
The spreadsheet contains the number of microbial reads mapped to more than 1500 pathogens, human genome reads, and unmapped reads.
The spreadsheet includes sample name, barcode number, total reads (raw reads), high quality reads (QC reads), spike-in control reads, human reads, pathogen reads, and unclassified reads. It also includes taxonomic information such as species and the number of reads aligned to each species.
The number of reads aligned to the human genome should be low, and the number of pathogen reads should be high.
ZymoBIOMICS™ Spike-in Control I
In the RUO version, no cut-offs are applied, making it unsuitable for clinical decision-making.
The clinical version identifies pathogens with a high possibility of presence in the sample and generates a PDF report with the results. In contrast, the RUO version does not evaluate pathogen possibility but instead provides a detailed spreadsheet. This spreadsheet includes the quantity of reads aligned to each pathogen and additional alignment metrics for each sample. Note that if a read aligns to multiple pathogens, it is randomly assigned to one of them.
If you need help interpreting your data, contact support@micronbrane.com.
Unclassified reads are reads that did not align to any genome (pathogens, human, or spike-ins).
PaRTI-Seq stands for Pathogen Real-Time Identification by Sequencing. It is our mNGS assay for pathogen identification, infectious disease, microbiome, transplant research and other applications consisting of three elements:
PaRTI-Seq can detect all microorganisms such as bacteria, fungi, viruses, and parasites in a sample.
Depending on a host cell’s status within its life cycle, PaRTI-Seq may be able to detect nucleic acids belonging to intracellular viruses and bacteria. However, confirming this would require further testing since the Devin Host Depletion filter captures nucleated host cells infected by intracellular microorganisms. As such, we are continuing analytical and clinical validation experiments to confirm that our filters can enrich cells infected with microorganisms. If you would like to start a collaborative project to test this, we invite you to join our Research Program.
Currently our Microbial Enrichment kit and downstream mNGS library kit detect only DNA viruses. Nonetheless, we are currently developing a separate workflow to detect RNA viruses. Join our newsletter and be notified the moment we launch the assay.
PaRTI-Seq is sequencer agnostic, however, our NGS library kit is currently only compatible with Illumina sequencers but we are quickly developing kits compatible with other sequencing platforms on the market.
Yes, PaRTI-Seq kits are available for both manual and automated protocols. Click here to learn how to integrate PaRTI-Seq into your mNGS workflows HERE.
Currently, the PaRTI-Seq workflow is for Research Use Only (RUO).
The Devin filter is used to remove nucleated cells from biological fluids. It is the only host depletion method that uses a zwitterionic membrane to selectively capture host nucleated cells, increasing the relative proportion of microbial pathogens.
The Devin filter leverages patented Zwitterionic Interface Ultra Self-assemble Coating (ZISC) technology to deplete host nucleated cells. ZISC technology forms a polymer cross-linked layer on the membrane with alternating positive and negative ionic patterns, creating a tightly bound hydration layer. The ionic interactions specifically target the hydrophilic proteins of host cells, retaining them within the filter, while allowing bacteria, viruses, fungi, and parasites to pass through unaltered.
No, it does not. The filter has a pore size of 15–20 μm, which is large enough to allow human cells and larger microorganisms, such as fungi, to pass through. Host cell depletion occurs due to the ionic technology rather than the pore size.
The Devin filter is compatible with all biological fluids.
The filter can be used with sample volumes ranging from 50 μl to 10 ml. To see an example of how Devin and PaRTI-Seq can work with low volumes read our App Note.
The filter has a pore size of 15-20 µm and a diameter of 25 mm. The outer shell is made of polypropylene, and the filter material is a hydrophilic, non-woven fabric.
For whole blood, place the sample in an EDTA tube. For swab samples, immerse the swab in 2-3 ml sterile phosphate-buffered solution (PBS) and stir for 10-15x. If the sample volume is less than 2 ml, top it up with PBS to 2 ml.
We currently recommend using the Devin filter for fresh samples (immediately after collection with storage NOT exceeding 6 hours at ambient temperature or 12 hours at 2-6°C). However, we are testing our products with frozen samples and we have some data on select types. If you plan to use frozen samples, please consult with us so we can share the data and make the best recommendation.
We generally recommend that clinical specimens be processed as soon as possible. When processed immediately, our Devin filter and PaRTI-Seq assay are compatible with any lab’s existing sample-batching policies for PCR and NGS-based assays . If you require your samples to be stored at any point, our kits allow for the following stopping points:
For Devin filter setup, sample-volume guidance, and workflow details, see the Devin Host Depletion Filter page. A written protocol is also available here.
Filter at a slow rate of approximately 1 ml/seconds.
Attach a sterile syringe to the female inlet side of the Devin filter. The inlet is wider and clear with grooves. The outlet is a male luer-lock (white).
Use only sterile syringes, tubes, and tips.
Dispose of the filter in accordance with local rules and regulations for hazardous materials.
No, the filter is disposable and cannot be re-sterilized or reused, including autoclaving or UV treatment.
Store unused filters in a dry place at room temperature (15–30°C).
The shelf life is 3 years.
Do not use filters past their expiration date, which is marked on both the packaging label and the filter container lid as “year-month.” These dates apply only to unopened filters. The lot number is located next to “LOT”. Use the filters promptly once opened.
Always wear appropriate protective equipment, such as masks and disposable gloves. Treat clinical samples as potentially infectious, especially those collected from at-risk patients. These samples should be labeled and handled under safe conditions. Use only sterile syringes, tubes, and tips to prevent nuclease contamination.
Before starting and after completion, spray the laboratory work area with Micronbrane Medical’s XNA Decontaminating Spray Cleaner or equivalent, then wipe with a lint-free cloth. This solution rapidly degrades nucleic acids and inactivates DNases, RNases, and surface enzymes.
For questions or concerns, email support@micronbrane.com.
The Devin Microbial DNA Enrichment Kit is for the extraction and purification of microbial genomic DNA from biological samples for analysis by Next-Generation Sequencing (NGS) or real-time PCR.
The kit includes: Devin Host Depletion filters, a pre-filled plate, elution buffer, incubation buffer, proteinase K, and lysozyme. The pre-filled plate contains: washing buffer 1A, washing buffer 1B, magnetic beads, washing buffer 2A, and washing buffer 2B.
All kit components, except lysozyme and proteinase K, can be stored at room temperature (15-30°C) until the expiration date. Lysozyme should be stored at -20°C upon arrival, although it is transported at room temperature. Proteinase K is stable at room temperature for short-term use but should be stored at -20°C for long-term storage.
You will need: high speed centrifuges, various sizes of tips and pipettes, syringes, Falcon tubes, disposable gloves, 95-100% ethanol, a vortex shaker, DNA low-binding tubes, a magnetic rack for 1.5 ml tubes, a thermomixer, and refrigerators at 4°C and -20°C.
Add 160 μl of elution buffer to the tube containing lysozyme to resuspend it.
After the final wash steps, open the cap of the [MB] tube and heat it at 45°C for up to 10 minutes to dry the magnetic beads. Do not exceed 10 minutes even if the pellet still looks slightly wet.
Add 50 μl of elution buffer to the [MB] tube, shake at 45°C for 5 minutes in a thermomixer, or gently pipette 5 times per minute for 5 minutes. Transfer the supernatant to a new DNA low binding tube.
Always wear appropriate protective equipment such as masks and disposable gloves. Treat clinical samples as potentially infectious. Avoid contact with reagents, and if contact occurs, flush with water immediately. Do not use bleach as the reagent contains guanidine salt.
Before starting and after completion, spray the laboratory work area with Micronbrane Medical’s XNA Decontaminating Spray Cleaner or equivalent, then wipe with a lint-free cloth.
Avoid vigorous shaking to prevent excessive foam. Avoid exposing opened reagents or plates to air. If reagents are colored, replace with a fresh plate. If the temperature is below 20°C, preheat the reagent-filled 96-well plate in an oven (42-60°C) for 5-10 minutes without removing the aluminum foil.
Dispose of all materials in accordance with local rules and regulations for hazardous materials.
Check that you have all the components, and if something is missing, contact support@micronbrane.com immediately and do not proceed with your project.
A system control is highly recommended. We recommend adding a spike-in control, such as ZymoBIOMICS™ Spike-in Control I, with known organisms to a no-template control reaction. We also recommend including a spike-in control in every reaction.
Reagents are all colorless and transparent, except for the magnetic beads. Colored reagents indicate contamination. Replace with a fresh plate before proceeding.
For questions or concerns, email support@micronbrane.com.
The Unison Ultralow DNA NGS Library Preparation Kit is used for generating libraries from very low DNA input. It is part of Micronbrane Medical’s Pathogen Real-Time Identification by Sequencing (PaRTI-Seq) Metagenomic Next-Generation Sequencing (mNGS) assay.
The kit is designed to prepare DNA libraries for sequencing on Illumina platforms, and it can be used for applications including whole genome sequencing, targeted sequencing by capture, and mNGS.
Depending on the kit type, components may include: Transposase Mix, 5x Reaction Buffer, 5x Stop Buffer, Amplification Mix, Index primer, and Purification beads. Some kits also include 2 sets of 24-well plates.
Store the purification beads at 4°C, and store all other reagents at -20°C. Do not use after the expiration date indicated on the outer packaging.
You will need disposable gloves, a disposable mask, pipettes and compatible pipette tips, a vortex, a microcentrifuge, absolute ethanol, nuclease-free water, a PCR thermal cycler, 1.5 ml microcentrifuge tubes, 1.5 ml DNA low binding tubes, 0.6 ml microcentrifuge tubes, a magnetic stand, a Qubit™ dsDNA High Sensitivity Assay Kit, and 0.2 ml PCR tubes.
The recommended input DNA is 1~5 ng or as low as 10 pg in a maximum volume of 8.6 μl for each reaction.
If you have difficulties, consider reducing the DNA input to 2 μl to mitigate potential PCR interference.
Quantify the extracted DNA using a Qubit dsDNA High Sensitivity Assay Kit or other fluorescence-based methods. Nanodrop and other absorbance-based DNA quantitation methods are not recommended.
Thaw the Transposase Mix, 5x Reaction Buffer, and 5x Stop Buffer at room temperature. Thaw the purification beads at room temperature for at least 30 minutes. Thaw the Amplification Mix and index primers on ice. Briefly vortex and spin down all the reagents before use.
Set up the reaction mix on ice, mix well by pipetting (do not vortex), and run the reaction in a thermal cycler according to the conditions in Table 2.
Add 5x Stop Buffer to the reaction, mix well, and put the tube back into the thermal cycler as shown in Table 3.
The number of cycles can be adjusted based on DNA input, refer to Table 6 .
Use Table 7 to calculate the volumes for beads 1 (V1) and beads 2 (V2), which depend on the target library size.
Add V1 of purification beads, mix, and incubate. Collect the supernatant. Add V2 of purification beads, mix, and incubate. Discard the supernatant. Wash the beads twice with 80% ethanol and let them air dry. Elute the DNA with nuclease-free water.
The constructed DNA library can be stored at -20°C.
If the final library is below the detection limit of Qubit, it may still be possible to sequence the library on the Illumina sequencing platform.
Clinical samples may be potentially infectious. Wear a mask, disposable gloves, and protective clothing. Avoid contact with eyes, skin, and clothing. If contact occurs, immediately flush the affected area with water. Use sterile, molecular biology-grade nuclease-free consumables to prevent sample degradation and contamination.
Dispose of all materials in accordance with local rules and regulations for hazardous materials.
For questions or concerns, email support@micronbrane.com.
It is a tool developed by Micronbrane Medical to analyze metagenomic Next-Generation Sequencing (mNGS) data, specifically using the PaRTI-Seq assay. This tool is designed to streamline the analysis of metagenomic data without requiring programming knowledge or special computers.
The user guide is found here.
We use FASTP for QA/QC, BWA MEM for aligning short reads, and Minimap2 for aligning long reads.
We leverage Amazon Web Services cloud computing and Nextflow pipelines to analyze samples quickly and scale with demand.
There is a single database containing over 1,500 pathogens. It’s currently not possible to run an analysis on a subset of this data.
The RUO database is updated on a yearly basis.
Data transfer and analysis are done through Micronbrane Medical’s web services hosted by AWS in Singapore.
You can use any computer with an internet connection to upload sample data and get results.
You need to create an account at the provided website, verify your account via email, and then you can access your project dashboard to begin your analyses. The website is: https://micronbrane.basepairtech.com/.
The RUO version is complementary, but you may need to contact support to get analysis codes.
Contact support@micronbrane.com, and they will email you another code.
Yes, you need to use the PaRTI-Seq Analysis code that came with your kit or was emailed to you. You can create an account without it, but you’ll need to add it later to run analyses.
Go to the drop-down menu in the top right corner, select “Billing and Coupons”, then the “Coupons” tab. Click “Activate coupon” and enter the code.
On the home page, click on “Sign up” and complete the form. You’ll need a password with at least one uppercase letter, one number, and one special character, between 12-16 characters long.
After registering, you will receive a verification email. Click the link in the email.
After verifying your account, click on the Micronbrane Medical logo.
Click on the yellow “Create new project” button or rename Project 1 on the dashboard.
Yes, you can add or remove samples from a project and have multiple analyses within the same project
You can upload samples by clicking “Add samples” in the center of your project screen, or via the “Upload” button, or “Add samples” in the Samples drop down menu.
Samples can be uploaded directly from your computer to the web app. You can also import samples from NCBI/GEO/SRA, BaseSpace, or an FTP/SFTP server.
Make sure that the sample IDs in your sample sheets are unique.
The web app accepts FASTQ and FASTA, either uncompressed or gzip compressed. Here is a detailed list of what the file extensions of those file types can look like: .fastq.gzip, .fq.gzip, .fastq.gz, .fq.gz, .fastq, .fq, .fasta.gzip, .fa.gzip, .fasta.gz, .fa.gz, .fasta, .fa.
It is recommended to leave “Sample Grouping” on automatic. You can also change the sample name. Make sure you select the correct project, platform, data type (PaRTI-Seq), and pipeline (SR-PaRTI-Seq or LR-PaRTI-Seq).
Click on the “Analyses” dropdown menu and select “New analysis” or “Start New Analysis” on the page
You can choose between long-read (LR-PaRTI-Seq) or short-read (SR-PaRTI-Seq) pipelines.
It’s best to use the short reads analysis for samples containing read lengths that are closer to 150 bp in length. Otherwise, the long reads analysis will be more appropriate.
Click the “Add samples” button, select your desired samples, and click “OK”.
Enter a suitable analysis name and then click on the “Run analysis” button.
A sample can take up to a half an hour to analyze. It can take up to 12 hours to process 24 samples in a single run.
The web app can process 24 samples per run and many runs can be started and run simultaneously.
Click on “Analyses,” then “View all analyses,” and select the specific analysis. In the “Input/Output” tab, click on “report.zip” to download the data.
The spreadsheet contains the number of microbial reads mapped to more than 1500 pathogens, human genome reads, and unmapped reads.
The spreadsheet includes sample name, barcode number, total reads (raw reads), high quality reads (QC reads), spike-in control reads, human reads, pathogen reads, and unclassified reads. It also includes taxonomic information such as species and the number of reads aligned to each species.
The number of reads aligned to the human genome should be low, and the number of pathogen reads should be high.
ZymoBIOMICS™ Spike-in Control I
In the RUO version, no cut-offs are applied, making it unsuitable for clinical decision-making.
The clinical version identifies pathogens with a high possibility of presence in the sample and generates a PDF report with the results. In contrast, the RUO version does not evaluate pathogen possibility but instead provides a detailed spreadsheet. This spreadsheet includes the quantity of reads aligned to each pathogen and additional alignment metrics for each sample. Note that if a read aligns to multiple pathogens, it is randomly assigned to one of them.
If you need help interpreting your data, contact support@micronbrane.com.
Unclassified reads are reads that did not align to any genome (pathogens, human, or spike-ins).
Micronbrane Medical technologies enrich our understanding of microorganisms through innovative metagenomic collection devices, novel host depletion, mNGS-grade reagents, advanced metagenomic sequencing assays, automation instrumentation, plus rapid bioinformatic software.
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