EARRINGS: an efficient and accurate adapter trimmer entails no a priori adapter sequences

Wang, Ting Hsuan; Huang, Cheng Ching; Hung, Jui-Hung

doi:10.1093/bioinformatics/btab025

Cited by 4 publications

(3 citation statements)

References 26 publications

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“…We downloaded the raw Chinese Moso bamboo data from BioProject accession PRJNA755164 [ 14 ] and used the sra-toolkit/2.10.4 ( https://github.com/ncbi/sra-tools ) to convert the data to fastq format. Adapters were then detected in EARRINGS/1.0.0 [ 43 ] using the default settings. Adapter trimming was not performed for samples in which no adapters were detected by EARRINGS.…”

Section: Methodsmentioning

confidence: 99%

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High genome heterozygosity revealed vegetative propagation over the sea in Moso bamboo

et al. 2023

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Background Moso bamboo (Phyllostachys edulis) is a typical East Asian bamboo that does not flower for > 60 years and propagates without seed reproduction. Thus, Moso bamboo can be propagated vegetatively, possibly resulting in highly heterozygous genetic inheritance. Recently, a draft genome of Moso bamboo was reported, followed by whole genome single nucleotide polymorphisms (SNP) analysis, which showed that the genome of Moso bamboo in China has regional characteristics. Moso bamboo in Japan is thought to have been introduced from China over the sea in 1736. However, it is unclear where and how Moso bamboo was introduced in Japan from China. Here, based on detailed analysis of heterozygosity in genome diversity, we estimate the spread of genome diversity and its pedigree of Moso bamboo. Results We sequenced the whole genome of Moso bamboo in Japan and compared them with data reported previously from 15 regions of China. Only 4.1 million loci (0.37% of the analyzed genomic region) were identified as polymorphic loci. We next narrowed down the number of polymorphic loci using several filters and extracted more reliable SNPs. Among the 414,952 high-quality SNPs, 319,431 (77%) loci were identified as heterozygous common to all tested samples. The result suggested that all tested samples were clones via vegetative reproduction. Somatic mutations may accumulate in a heterozygous manner within a single clone. We examined common heterozygous loci between samples from Japan and elsewhere, from which we inferred that an individual closely related to the sample from Fujian, China, was introduced to Japan across the sea without seed reproduction. In addition, we collected 16 samples from four nearby bamboo forests in Japan and performed SNP and insertion/deletion analyses using a genotyping by sequencing (GBS) method. The results suggested that a small number of somatic mutations would spread within and between bamboo groves. Conclusions High heterozygosity in the genome-wide diversity of Moso bamboo implies the vegetative propagation of Moso bamboo from China to Japan, the pedigree of Moso bamboo in Japan, and becomes a useful marker to approach the spread of genome diversity in clonal plants.

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Section: Methodsmentioning

confidence: 99%

“…com/ ncbi/ sra-tools) to convert the data to fastq format. Adapters were then detected in EARRINGS/1.0.0 [43] using the default settings. Adapter trimming was not performed for samples in which no adapters were detected by EARRINGS.…”

Section: Wgs and Detection Of The High-quality Snpsmentioning

confidence: 99%

High genome heterozygosity revealed vegetative propagation over the sea in Moso bamboo

et al. 2023

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“…Several tools have been developed to identify adapter sequences from raw reads. For examples, Atropos [ 21 ], fastp [ 22 ], DNApi [ 23 ], and EARRINGS [ 24 ] count k-mers in reads to infer adapter sequences. However, k-mer counting methods do not consider random-mers at each side of the ligation site, such as the random tetramer at both the 5’ and 3’ ends produced by the NEXTFLEX Kit ( Fig 1c ).…”

Section: Introductionmentioning

confidence: 99%

FindAdapt: A python package for fast and accurate adapter detection in small RNA sequencing

Chen,

Wang,

Shyr

et al. 2024

PLoS Comput Biol

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Adapter trimming is an essential step for analyzing small RNA sequencing data, where reads are generally longer than target RNAs ranging from 18 to 30 bp. Most adapter trimming tools require adapter information as input. However, adapter information is hard to access, specified incorrectly, or not provided with publicly available datasets, hampering their reproducibility and reusability. Manual identification of adapter patterns from raw reads is labor-intensive and error-prone. Moreover, the use of randomized adapters to reduce ligation biases during library preparation makes adapter detection even more challenging. Here, we present FindAdapt, a Python package for fast and accurate detection of adapter patterns without relying on prior information. We demonstrated that FindAdapt was far superior to existing approaches. It identified adapters successfully in 180 simulation datasets with diverse read structures and 3,184 real datasets covering a variety of commercial and customized small RNA library preparation kits. FindAdapt is stand-alone software that can be easily integrated into small RNA sequencing analysis pipelines.

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MiR34 contributes to spinal muscular atrophy and AAV9-mediated delivery of MiR34a ameliorates the motor deficits in SMA mice

Chen¹,

Chang²,

Wu³

et al. 2023

Molecular Therapy - Nucleic Acids

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EARRINGS: an efficient and accurate adapter trimmer entails no a priori adapter sequences

Cited by 4 publications

References 26 publications

High genome heterozygosity revealed vegetative propagation over the sea in Moso bamboo

High genome heterozygosity revealed vegetative propagation over the sea in Moso bamboo

FindAdapt: A python package for fast and accurate adapter detection in small RNA sequencing

MiR34 contributes to spinal muscular atrophy and AAV9-mediated delivery of MiR34a ameliorates the motor deficits in SMA mice

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