A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics
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PROVIDER: PRJEB65885 | ENA |
REPOSITORIES: ENA
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Project description:LocusMasterTE: long-read assisted short-read TE quantification [short]
| PRJNA935371 | ENA
Project description:With an ability to compromise genome integrity, transposable elements (TEs) have significant associations with human diseases. Short-read sequencing has been used to study the expression of TEs; however, the highly repetitive nature of these elements makes multimapping a critical issue. Here we implement LocusMasterTE, an improved quantification method by integrating long-read sequencing. Introducing computed transcript per million(TPM) counts from long-read sequencing as prior distribution during Expectation-Maximization(EM) model in short-read TE quantification, multi-mapped reads are re-assigned to correct expression values. Based on simulated short reads, LocusMasterTE outperforms current quantitative approaches and is significantly favorable in capturing newly inserted TEs. We also verified that TEs quantified by LocusMasterTE clearly related to euchromatins and heterochromatins in cell line samples. With LocusMasterTE we anticipate that more accurate quantification can be performed, allowing novel functions of TEs to be uncovered.
2023-09-01 | GSE225380 | GEO
Project description:With an ability to compromise genome integrity, transposable elements (TEs) have significant associations with human diseases. Short-read sequencing has been used to study the expression of TEs; however, the highly repetitive nature of these elements makes multimapping a critical issue. Here we implement LocusMasterTE, an improved quantification method by integrating long-read sequencing. Introducing computed transcript per million(TPM) counts from long-read sequencing as prior distribution during Expectation-Maximization(EM) model in short-read TE quantification, multi-mapped reads are re-assigned to correct expression values. Based on simulated short reads, LocusMasterTE outperforms current quantitative approaches and is significantly favorable in capturing newly inserted TEs. We also verified that TEs quantified by LocusMasterTE clearly related to euchromatins and heterochromatins in cell line samples. With LocusMasterTE we anticipate that more accurate quantification can be performed, allowing novel functions of TEs to be uncovered.
2023-09-01 | GSE225377 | GEO
Project description:Evaluation of short-read-only, long-read-only, and hybrid assembly approaches on metagenomic samples demonstrating how they affect gene and protein prediction which is relevant for downstream functional analyses. For a human gut microbiome sample, we use complementary metatranscriptomic, and metaproteomic data to evaluate the metagenomic-based protein predictions.
2022-02-17 | PXD025505 | Pride
Project description:LocusMasterTE: long-read assisted short-read RNA-seq TE quantification [long]
| PRJNA935368 | ENA
Project description:BackgroundDifferent high-throughput nucleic acid sequencing platforms are currently available but a trade-off currently exists between the cost and number of reads that can be generated versus the read length that can be achieved.Methodology/principal findingsWe describe an experimental and computational pipeline yielding millions of reads that can exceed 200 bp with quality scores approaching that of traditional Sanger sequencing. The method combines an automatable gel-less library construction step with paired-end sequencing on a short-read instrument. With appropriately sized library inserts, mate-pair sequences can overlap, and we describe the SHERA software package that joins them to form a longer composite read.Conclusions/significanceThis strategy is broadly applicable to sequencing applications that benefit from low-cost high-throughput sequencing, but require longer read lengths. We demonstrate that our approach enables metagenomic analyses using the Illumina Genome Analyzer, with low error rates, and at a fraction of the cost of pyrosequencing.
| S-EPMC2911387 | biostudies-literature
Project description:DNA sequencing is a critical tool in modern biology. Over the last two decades, it has been revolutionized by the advent of massively parallel sequencing, leading to significant advances in genome and transcriptome sequencing of various organisms. Nevertheless, challenges such as accuracy, lack of competitive options and prohibitive costs associated with high throughput parallel short-read sequencing persist. Here, we conduct a comparative analysis between the Element Biosciences AVITI platform and its counterpart the Illumina NextSeq platform, testing DNA and RNA short-read sequencing, as well as synthetic long-read sequencing for single cells and RNA transcripts.
2024-08-19 | GSE246832 | GEO
Project description:DNA sequencing is a critical tool in modern biology. Over the last two decades, it has been revolutionized by the advent of massively parallel sequencing, leading to significant advances in genome and transcriptome sequencing of various organisms. Nevertheless, challenges such as accuracy, lack of competitive options and prohibitive costs associated with high throughput parallel short-read sequencing persist. Here, we conduct a comparative analysis between the Element Biosciences AVITI platform and its counterpart the Illumina NextSeq platform, testing DNA and RNA short-read sequencing, as well as synthetic long-read sequencing for single cells and RNA transcripts.
2024-08-19 | GSE246830 | GEO
Project description:Short-read nascent RNA sequencing from S. pombe
| PRJNA413497 | ENA
Project description:Dindel: Accurate indel calls from short read data
| PRJEB2293 | ENA