ArticleGenome biology2014
Determining the quality and complexity of next-generation sequencing data without a reference genome.
Article in Genome biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
12 citing papers in PubMed.
- Biostatistical Aspects of Whole Genome Sequencing Studies: Preprocessing and Quality Control.Biometrical journal. Biometrische Zeitschrift · 2024Article
- Circular RNAs in the human brain are tailored to neuron identity and neuropsychiatric disease.Nature communications · 2023Article
- Circular RNAs in the human brain are tailored to neuron identity and neuropsychiatric disease.bioRxiv : the preprint server for biology · 2023Article
- A systematic bioinformatics approach for large-scale identification and characterization of host-pathogen shared sequences.BMC genomics · 2021Article
- Factorial estimating assembly base errors usingNAR genomics and bioinformatics · 2020Article
- Streaming histogram sketching for rapid microbiome analytics.Microbiome · 2019Article
- Hierarchical Clustering of DNA k-mer Counts in RNAseq Fastq Files Identifies Sample Heterogeneities.International journal of molecular sciences · 2018Article
- Enhancers active in dopamine neurons are a primary link between genetic variation and neuropsychiatric disease.Nature neuroscience · 2018Article
- Genome-reconstruction for eukaryotes from complex natural microbial communities.Genome research · 2018Article
- KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies.Bioinformatics (Oxford, England) · 2017Article
- Identity by descent fine mapping of familial adult myoclonus epilepsy (FAME) to 2p11.2-2q11.2.Human genetics · 2016Article
- Genomic resources for wild populations of the house mouse, Mus musculus and its close relative Mus spretus.Scientific data · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We describe an open-source kPAL package that facilitates an alignment-free assessment of the quality and comparability of sequencing datasets by analyzing k-mer frequencies. We show that kPAL can detect technical artefacts such as high duplication rates, library chimeras, contamination and differences in library preparation protocols. kPAL also successfully captures the complexity and diversity of microbiomes and provides a powerful means to study changes in microbial communities. Together, these features make kPAL an attractive and broadly applicable tool to determine the quality and comparability of sequence libraries even in the absence of a reference sequence. kPAL is freely available at https://github.com/LUMC/kPAL webcite.
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Identifiers
What OpenQuestion holds
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.