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Loop Genomics

1 Order Completed
San Jose, California, US

About Loop Genomics

Divison of: Y Combinator

Loop Genomics is the only hardware-free synthetic long read sequencing approach that transforms any short read sequencer into a single molecule long read sequencer.

The company has developed proprietary sample prep and software that tag DNA/RNA molecules with DNA barcodes and copies and pastes those barcodes... Show more »

Loop Genomics is the only hardware-free synthetic long read sequencing approach that transforms any short read sequencer into a single molecule long read sequencer.

The company has developed proprietary sample prep and software that tag DNA/RNA molecules with DNA barcodes and copies and pastes those barcodes intra-molecularly throughout long molecules. Once barcodes are distributed intra-molecularly, libraries are converted into a standard short read library and sequenced on any short read sequencer.

After sequencing, reads with the same barcodes are grouped together and assembled back into the longer molecules that were tagged by those barcode using Loop's software. Loop sequencing is used to assemble genomes, transcriptomes or targeted amplicons from long reads, providing highly accurate, single molecule long read data for any application and leveraging your existing short read infrastructure.

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Our Services (7)


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Fungal Community Analysis

Price on request

Mycobiome - 18S ITS1 & ITS2 rRNA Sequencing and data analysis

While high-throughput sequencing methods are revolutionizing fungal ecology, recovering accurate estimates of species richness and abundance has proven elusive.

With short read technology researchers have had to chose to... Show more »

Mycobiome - 18S ITS1 & ITS2 rRNA Sequencing and data analysis

While high-throughput sequencing methods are revolutionizing fungal ecology, recovering accurate estimates of species richness and abundance has proven elusive.

With short read technology researchers have had to chose to use only ITS1 or ITS2 or 18S as a way to classify.

With Loop's long-read technology of short read Illumina sequencers we now let you use the data from all three markers as a superior way to classify your samples.  

We maximized this classification power by combining all three of the common databases bioinformatically into one supercharged classifying engine to super charge your long read data.

We will use our LoopSeq single molecule-counting long-read Mycobiome 18S ITS1 & ITS2 Ribosomal RNA kit to sequence your mycobiome samples to determine the type and relative abundance of fungal species. We can accept purified DNA from gut, skin, soil, marine or other sources.

Advantages:
 • Higher sensitivity than other services as we interrogate the 18S ITS1 & ITS2 region and the same time with our single molecule counting long-read technology
 • 40x lower error when compared to Illumina library prep
 • Cost-effective
 • Fast turnaround 

Region coverage:
2.5Kb contiguous 18S ITS1 & ITS2 

Deliverables:
Our standard analysis includes CSV files with (1) Single molecule quantification of abundance based on Unique molecular Identifiers (UMI's), eliminating amplification biases, (2) Reference based taxonomic classification based on nine variable regions (V1-V9 data in 16S and 18S) and long-reads in Metagenomic sequencing, (3) OTU tables, (4) Rarefaction analysis, (5) RAD analysis, as well as pie chart visualizations of classification and quantification.(5) Raw data as FASTA and FASTQ files.

Turn Around Time: 3 weeks 

Sample Submission: High quality genomic DNA , a minimum of 10ng as quantified by Qubit 2.0, or 1ng DNA from skin

minimum sample amount: 8

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16S rRNA Sequencing

Starting at CAD$199.00 per sample

Service description:

We will use our LoopSeq single molecule-counting long-read 16S Ribosomal RNA kit to sequence your microbiome samples to determine the type and relative abundance of bacterial and archaeal species. We can accept purified DNA from gut, skin, soil, marine or other sources.

Advantages:

• Higher sensitivity... Show more »

Service description:

We will use our LoopSeq single molecule-counting long-read 16S Ribosomal RNA kit to sequence your microbiome samples to determine the type and relative abundance of bacterial and archaeal species. We can accept purified DNA from gut, skin, soil, marine or other sources.

Advantages:

• Higher sensitivity than other 16s services as we interrogate the entire 16s molecule V1-V9 with our single molecule counting long-read technology
• 40x lower error to Illumina library prep
• Cost-effective
• Fast turnaround

Region coverage:

Full 16s molecule, all V1-V9 variable regions

Deliverables:

Our standard analysis includes CSV files with (1) Single molecule quantification of abundance based on Unique molecular Identifiers (UMI's), eliminating amplification biases, (2) Reference based taxonomic classification based on nine variable regions (V1-V9 data in 16S and 18S) and long-reads in Metagenomic sequencing, (3) OTU tables, (4) Rarefaction analysis, (5) RAD analysis, as well as pie chart visualizations of classification and quantification.(5) Raw data as FASTA and FASTQ files

Turn Around Time: 3 weeks
Sample Submission: High quality genomic DNA , a minimum of 10ng as quantified by Qubit 2.0, or 1ng DNA from skin

minimum sample amount: 8

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Transcriptome Sequencing and Profiling

Starting at $299.00 per sample

Service description:

We will use our LoopSeq single-molecule counting long-read sequencing technology to for Transcriptome sequencing of your samples.

Advantages:

Unlike RNASeq which only counts transcripts we will not only provide transcript counting results but provide unique iso-form detection, enabled by our long-read... Show more »

Service description:

We will use our LoopSeq single-molecule counting long-read sequencing technology to for Transcriptome sequencing of your samples.

Advantages:

Unlike RNASeq which only counts transcripts we will not only provide transcript counting results but provide unique iso-form detection, enabled by our long-read technology, as well.

Requirements:
10ng of total RNA

Deliverables:

Our standard analysis includes FastQ and FastA files with the reconstructed mRNA long reads. Additionally, each RNA sample includes a downstream analysis summarized in a CSV file that includes (1) Single molecule quantification of mRNA abundance based on Unique molecular Identifiers (UMI's), eliminating amplification biases and providing accurate gene expression quantification, (2) Alignment of the mRNA long reads to RefSeq and a complete statistical report on each aligned molecule. Additionally, alignment to custom databases is available upon request.

8 sample minimum requirement

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Illumina HiSeq 2500 Illumina NextSeq 500 Illumina NovaSeq 6000 RNA sequencing Illumina

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DNA Sequencing

Starting at $299.00 per sample

Service Description:

We will use our LoopSeq single-molecule counting long-read sequencing technology to for DNA sequencing of your samples. We will not only provide single-molecule counting results for true abundance but provide long-read output as enable by our unique technology.
Input is any dsDNA. Input can be a long-range... Show more »

Service Description:

We will use our LoopSeq single-molecule counting long-read sequencing technology to for DNA sequencing of your samples. We will not only provide single-molecule counting results for true abundance but provide long-read output as enable by our unique technology.
Input is any dsDNA. Input can be a long-range PCR product, Amplicon, etc.

Requirements: 10ng of total DNA

Deliverables:

Our standard analysis includes FastQ and FastA files with the reconstructed DNA long reads from the barcoded short treads. Additionally, each sample includes downstream analysis summarized in a CSV files with alignment of each reconstructed DNA molecule and a reference database.

8 sample minimum requirement

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Illumina HiSeq 2000 Illumina NextSeq 500 Illumina NovaSeq 6000 DNA sequencing Illumina

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Metagenomics

Starting at $299.00 per sample

Service Description :

We will use our LoopSeq single-molecule counting long-read platform to perform Metagenomics sequencing on your samples. We will use "shotgun" or PCR directed sequencing to get largely unbiased samples of all genes from all the members of the sampled communities from your samples.

Advantages:
• Higher... Show more »

Service Description :

We will use our LoopSeq single-molecule counting long-read platform to perform Metagenomics sequencing on your samples. We will use "shotgun" or PCR directed sequencing to get largely unbiased samples of all genes from all the members of the sampled communities from your samples.

Advantages:
• Higher sensitivity
• Low error
• Lower cost than other platforms
• Fast turnaround
Region coverage are the whole genome

Deliverables:
• Raw data as FASTA and FASTQ files
•denovo assembly per request

Turn Around Time:
• 3 weeks

Sample Submission:
• High quality genomic DNA, a minimum of 10 ng as quantified by Qubit 2.0.
We can also take 1 ng if skin samples are the input.

minimum sample amount: 24

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Illumina HiSeq 2500 Illumina NextSeq 500 Illumina NovaSeq 6000 Illumina

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Whole Exome Sequencing (WES)

Price on request

Service description:
We will use our LoopSeq single molecule long-read technology to perform Whole Exome Sequencing (WES) on your samples. WES is thought by many to be an efficient way to understand the genetic cause of diseases or conditions. The inherent low error and single-molecule counting found in our technology on... Show more »

Service description:
We will use our LoopSeq single molecule long-read technology to perform Whole Exome Sequencing (WES) on your samples. WES is thought by many to be an efficient way to understand the genetic cause of diseases or conditions. The inherent low error and single-molecule counting found in our technology on Illumina sequencers means that we provide a very cost-effective and accurate WES service.
• Advantages:
a) Low cost
b) Low error
c) Short TAT
• Service grade: Research Use Only
• Human exons in approximately 23,000 genes.
• Deliverables:
a) FASTA, FASTQ and additional bioinformatics analysis including variant annotation
• Sequencing depth:
a) Mean depth of coverage: ≥ 80x
b) 93% of exons covered at ≥ 25x depth

Higher coverage available for additional charges, please inquire for details.
• TurnAroundTime: 3 weeks
• Sample requirements:
High quality genomic human DNA: a minimum of 10 nanogram as quantified by Qubit 2.0

• Sequencing platforms:
a) Illumina NextSeq paired-end 2x150 bp reads
b) Illumina HiSeq paired-end 2x150 bp reads

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Whole Genome Sequencing

Price on request

Microbial genome long-read sequencing service using LoopSeq.
De novo long-read sequencing is performed without prior knowledge of the samples. We will deliver long-read FASTA and FASTQ files and do sequence assembly.
• Advantages:
a) Low cost as we leverage Illumina sequencers but our kits transform them into single molecule... Show more »

Microbial genome long-read sequencing service using LoopSeq.
De novo long-read sequencing is performed without prior knowledge of the samples. We will deliver long-read FASTA and FASTQ files and do sequence assembly.
• Advantages:
a) Low cost as we leverage Illumina sequencers but our kits transform them into single molecule long-read machines.
b) Our long-read technology provides 40x lower error rate than traditional Illumina sequencing and error rates orders of magnitude lower than other long-read technologies. Our single-molecule counting gets rid of PCR which means more accurate data.
c) Short TAT
• Service grade: Research Use Only
• Bacterial whole genome
• Deliverables:
FASTA, FASTQ and bioinformatics analysis
• Sequencing depth:
Mean depth of coverage: 100x for genomes ~5Mb in size
Higher coverage available for additional charges, please inquire

• Turn Around Time: 3 weeks

• Sample requirements:
High quality genomic human DNA: a minimum of 10 nanogram as quantified by Qubit 2.0

We'll run your samples on an Illumina platform, Paired-end150 bp .

minimum sample amount: 3

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Illumina HiSeq 2500 Illumina NovaSeq 6000 Illumina

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