ArticleMicrobial genomics2020
Read trimming has minimal effect on bacterial SNP-calling accuracy.
Article in Microbial genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
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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.
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Who cites it
20 citing papers in PubMed.
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- Metagenomic characterization of the virome of Aedes albopictus in Anhui Province, China, with phylogenetic analysis of CRESS-DNA viruses and Parvoviridae.Virus genes · 2026Article
- Genome-wide association study of molecular markers related to keel length in a specialized strain of yellow feathered broilers.Poultry science · 2026Article
- The metastasis landscape ofFrontiers in immunology · 2026Article
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- Evaluation of Illumina and Oxford Nanopore Sequencing for the Study of DNA Methylation in Alzheimer's Disease and Frontotemporal Dementia.International journal of molecular sciences · 2025Review
- Peripheral blood microbiome signature and Mycobacterium tuberculosis-derived rsRNA as diagnostic biomarkers for tuberculosis in human.Journal of translational medicine · 2025Article
- Whole genome sequence data ofData in brief · 2025Article
- SNiPgenie: a tool for microbial SNP site detection from whole-genome sequencing data.Access microbiology · 2025Article
- Mission SpaceX CRS-16 RRRM-1 space flight induced skin genomic plasticity via an epigenetic trigger.iScience · 2024Article
- PRDM14 extinction enables the initiation of trophoblast stem cell formation.Cellular and molecular life sciences : CMLS · 2024Article
- Bioinformatics of germline variant discovery for rare disease diagnostics: current approaches and remaining challenges.Briefings in bioinformatics · 2024Review
- Discovering a novel glycosyltransferase geneFrontiers in microbiology · 2024Article
- AI-enabled pipeline for virus detection, validation, and SNP discovery from next-generation sequencing data.Frontiers in genetics · 2024Article
- Identification of RNU44 as an Endogenous Reference Gene for Normalizing Cell-Free RNA in Tuberculosis.Open forum infectious diseases · 2022Article
- Draft Genomic Sequences of Four Pseudomonas spp. and aMicrobiology resource announcements · 2022Article
- Genomic New Insights Into Emergence and Clinical Therapy of Multidrug-ResistantFrontiers in microbiology · 2021Article
Corrections and comments
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Authors and funding
1 author.
Funding
Abstract
Read alignment is the central step of many analytic pipelines that perform variant calling. To reduce error, it is common practice to pre-process raw sequencing reads to remove low-quality bases and residual adapter contamination, a procedure collectively known as 'trimming'. Trimming is widely assumed to increase the accuracy of variant calling, although there are relatively few systematic evaluations of its effects and no clear consensus on its efficacy. As sequencing datasets increase both in number and size, it is worthwhile reappraising computational operations of ambiguous benefit, particularly when the scope of many analyses now routinely incorporates thousands of samples, increasing the time and cost required. Using a curated set of 17 Gram-negative bacterial genomes, this study initially evaluated the impact of four read-trimming utilities (Atropos, fastp, Trim Galore and Trimmomatic), each used with a range of stringencies, on the accuracy and completeness of three bacterial SNP-calling pipelines. It was found that read trimming made only small, and statistically insignificant, increases in SNP-calling accuracy even when using the highest-performing pre-processor in this study, fastp. To extend these findings, >6500 publicly archived sequencing datasets from
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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.