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. 2024 Oct 14;17(1):308.
doi: 10.1186/s13104-024-06951-0.

Sequence-matching adapter trimmers generate consistent quality and assembly metrics for Illumina sequencing of RNA viruses

Grace Nabakooza  1   2 , Darlene D Wagner  3 , Nehalraza Momin  3 , Rachel L Marine  4 , William C Weldon  4 , M Steven Oberste  4
Affiliations

Sequence-matching adapter trimmers generate consistent quality and assembly metrics for Illumina sequencing of RNA viruses

Grace Nabakooza et al. BMC Res Notes. .

Abstract

Trimming adapters and low-quality bases from next-generation sequencing (NGS) data is crucial for optimal analysis. We evaluated six trimming programs, implementing five different algorithms, for their effectiveness in trimming adapters and improving quality, contig assembly, and single-nucleotide polymorphism (SNP) quality and concordance for poliovirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and norovirus paired data sequenced on Illumina iSeq and MiSeq platforms. Trimmomatic and BBDuk effectively removed adapters from all datasets, unlike FastP, AdapterRemoval, SeqPurge, and Skewer. All trimmers improved read quality (Q ≥ 30, 87.8 - 96.1%) compared to raw reads (83.6 - 93.2%). Trimmers implementing traditional sequence-matching (Trimmomatic and AdapterRemoval) and overlapping algorithm (FastP) retained the highest-quality reads. While all trimmers improved the maximum contig length and genome coverage for iSeq and MiSeq viral assemblies, BBDuk-trimmed reads assembled the shortest contigs. SNP concordance was consistently high (> 97.7 - 100%) across trimmers. However, BBDuk-trimmed reads had the lowest quality SNPs. Overall, the two adapter trimmers that utilized the traditional sequence-matching algorithm performed consistently across the viral datasets analyzed. Our findings guide software selection and inform future versatile trimmer development for viral genome analysis.

Keywords: Adapter trimming; De novo assembly; Illumina; Next-generation sequencing; Quality control; RNA viruses.

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Conflict of interest statement

The authors declare no competing interests.

The authors declare no conflicting interests.

Figures

Fig. 1
Fig. 1
Differences in percentage residual adapters between iSeq vs. MiSeq poliovirus, severe acute respiratory syndrome coronavirus 2, and norovirus reads, grouped by the trimmer. The median is shown as black bars, while the gray bars show the mean and standard error interval. Only statistically significant differences are indicated with corresponding p-values. Abbreviations: Polio is for poliovirus, Noro for norovirus, and SC2 for severe acute respiratory syndrome coronavirus 2
Fig. 2
Fig. 2
Mean (average) read lengths of raw and trimmed iSeq (red) and MiSeq (blue) reads for poliovirus (A), severe acute respiratory syndrome coronavirus 2 (B), and norovirus (C) datasets. Abbreviations: SC2 for severe acute respiratory syndrome coronavirus 2
See this image and copyright information in PMC

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