ArticlePloS one2008
The long march: a sample preparation technique that enhances contig length and coverage by high-throughput short-read sequencing.
Article in PloS one, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
20 citing papers in PubMed, 30 citations in OpenAlex.
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- Cross-species transmission of a novel adenovirus associated with a fulminant pneumonia outbreak in a new world monkey colony.PLoS pathogens · 2011Article
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- NSR-seq transcriptional profiling enables identification of a gene signature of Plasmodium falciparum parasites infecting children.The Journal of clinical investigation · 2011Article
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- HMMSplicer: a tool for efficient and sensitive discovery of known and novel splice junctions in RNA-Seq data.PloS one · 2010Article
- A metagenomic analysis of pandemic influenza A (2009 H1N1) infection in patients from North America.PloS one · 2010Article
- Unlocking short read sequencing for metagenomics.PloS one · 2010Article
- Cultivation and serological characterization of a human Theiler's-like cardiovirus associated with diarrheal disease.Journal of virology · 2010Article
- New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.Molecular microbiology · 2010Article
- Genomics and integrated systems biology in Plasmodium falciparum: a path to malaria control and eradication.Parasite immunologyReview
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 1 institution in 1 country.
Funding
Abstract
High-throughput short-read technologies have revolutionized DNA sequencing by drastically reducing the cost per base of sequencing information. Despite producing gigabases of sequence per run, these technologies still present obstacles in resequencing and de novo assembly applications due to biased or insufficient target sequence coverage. We present here a simple sample preparation method termed the "long march" that increases both contig lengths and target sequence coverage using high-throughput short-read technologies. By incorporating a Type IIS restriction enzyme recognition motif into the sequencing primer adapter, successive rounds of restriction enzyme cleavage and adapter ligation produce a set of nested sub-libraries from the initial amplicon library. Sequence reads from these sub-libraries are offset from each other with enough overlap to aid assembly and contig extension. We demonstrate the utility of the long march in resequencing of the Plasmodium falciparum transcriptome, where the number of genomic bases covered was increased by 39%, as well as in metagenomic analysis of a serum sample from a patient with hepatitis B virus (HBV)-related acute liver failure, where the number of HBV bases covered was increased by 42%. We also offer a theoretical optimization of the long march for de novo sequence assembly.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.