long read amplicon sequencing service  (Plasmidsaurus)

Journal: bioRxiv

Article Title: Ultra-accurate Microbial Amplicon Sequencing Directly from Complex Samples with Synthetic Long Reads

doi: 10.1101/2020.07.07.192286

Figure Lengend Snippet: The abundances of all ASVs identified by LoopSeq and default DADA2 in the Zymo mock community. All abundances are scaled to the abundance of the corresponding genome in the amplified 16S rRNA gene data. The near-integer values of all genome-scaled abundances are consistent with each ASV representing a unique allele present in the multiple copies of the 16S rRNA gene present in the genomes of these strains.

Article Snippet: Loop Genomics has recently commercialized synthetic long-read amplicon sequencing under the LoopSeq product line which is available both as a kit and a laboratory service (Loop Genomics, CA).

Techniques: Amplification

Journal: bioRxiv

Article Title: Ultra-accurate Microbial Amplicon Sequencing Directly from Complex Samples with Synthetic Long Reads

doi: 10.1101/2020.07.07.192286

Figure Lengend Snippet: The rates of LoopSeq point errors by position in read, type (in/del/substitution) and quality score.

Article Snippet: Loop Genomics has recently commercialized synthetic long-read amplicon sequencing under the LoopSeq product line which is available both as a kit and a laboratory service (Loop Genomics, CA).

Techniques:

Journal: bioRxiv

Article Title: Ultra-accurate Microbial Amplicon Sequencing Directly from Complex Samples with Synthetic Long Reads

doi: 10.1101/2020.07.07.192286

Figure Lengend Snippet: Error types and rates in LoopSeq data. a) Schematic description of three error types: point errors, chimeras, introgressions. b) The fraction of each error type as a function of expected error quality filter threshold. The red line shows the fraction of LoopSeq reads removed as a function of the filter threshold.

Article Snippet: Loop Genomics has recently commercialized synthetic long-read amplicon sequencing under the LoopSeq product line which is available both as a kit and a laboratory service (Loop Genomics, CA).

Techniques:

Journal: bioRxiv

Article Title: Ultra-accurate Microbial Amplicon Sequencing Directly from Complex Samples with Synthetic Long Reads

doi: 10.1101/2020.07.07.192286

Figure Lengend Snippet: The fraction of error-free amplicon sequencing reads of different lengths using commercially available long-read sequencing technologies. Points represent observations from measurements of defined communities (the Zymo mock community) or single-strain isolates (fungal and bacterial isolates) that were reported in this manuscript for LoopSeq, and that were reported in for PacBio CCS reads. The 16S rRNA and fungal 18S-ITS data is from traditional amplicon sequencing of a single genetic region (Methods). The LoopSeq genomic amplicon data is based on LoopSeq sequencing of randomly amplified regions of the genome of several bacteria (Methods). Lines represent the expected error-free fraction based on measurements of the error rates in 16S rRNA gene amplicon sequencing data, and assuming a constant per-base error rate. The Oxford Nanopore line is based on the per-base error-rate of 6% reported by the manufacturer for the R10 chemistry.

Article Snippet: Loop Genomics has recently commercialized synthetic long-read amplicon sequencing under the LoopSeq product line which is available both as a kit and a laboratory service (Loop Genomics, CA).

Techniques: Amplification, Sequencing

Journal: bioRxiv

Article Title: Ultra-accurate Microbial Amplicon Sequencing Directly from Complex Samples with Synthetic Long Reads

doi: 10.1101/2020.07.07.192286

Figure Lengend Snippet: PCoA ordination of the total community compositions of three human fecal samples as measured by LoopSeq and PacBio full-length 16S rRNA gene sequencing. The community compositions measured by each technology were highly similar, leading to the data points on this ordination being highly overlapping for each sample. PacBio CCS measurements were made using two different sequencing chemistries as indicated in the legend parentheticals.

Article Snippet: Loop Genomics has recently commercialized synthetic long-read amplicon sequencing under the LoopSeq product line which is available both as a kit and a laboratory service (Loop Genomics, CA).

Techniques: Sequencing

Journal: bioRxiv

Article Title: Ultra-accurate Microbial Amplicon Sequencing Directly from Complex Samples with Synthetic Long Reads

doi: 10.1101/2020.07.07.192286

Figure Lengend Snippet: The number of substitution differences between DADA2-denoised ASVs and the next closest ASV that are in conserved vs. variable regions of the 16S gene, in LoopSeq data from three human fecal samples. Approximately 80% of nucleotide positions are conserved, thus if substitution patterns were random (as might be the case if they were caused by sequencing errors) then points should fall on the dashed red line.

Article Snippet: Loop Genomics has recently commercialized synthetic long-read amplicon sequencing under the LoopSeq product line which is available both as a kit and a laboratory service (Loop Genomics, CA).

Techniques: Sequencing

Journal: bioRxiv

Article Title: Ultra-accurate Microbial Amplicon Sequencing Directly from Complex Samples with Synthetic Long Reads

doi: 10.1101/2020.07.07.192286

Figure Lengend Snippet: Foodborne pathogens detected in retail meat rinse samples. a) The species and relative abundance of six common foodborne pathogen species were determined from full-length LoopSeq 16S sequencing of six retail meat samples. Campylobacter and Listeria monocytogenes do not appear in these samples. b) Nine distinct alleles of the 16S rRNA gene were detected in the C. perfringens strain present in sample GT1. The first allele was present at roughly twice the abundance of the others, consistent with it having two copies in the genome while the rest have only one copy. C. perfringens has 10 copies of the 16S rRNA gene in its genome. Only the V2 region is shown for visual simplicity.

Article Snippet: Loop Genomics has recently commercialized synthetic long-read amplicon sequencing under the LoopSeq product line which is available both as a kit and a laboratory service (Loop Genomics, CA).

Techniques: Sequencing