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ReadItAndKeep: Rapid decontamination of SARS-CoV-2 sequencing reads

bioRxiv, ISSN: 2692-8205
2022
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  • Citations
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Article Description

Viral sequence data from clinical samples frequently contain human contamination, which must be removed prior to sharing for legal and ethical reasons. To enable host read removal for SARS-CoV-2 sequencing data on low-specification laptops, we developed ReadItAndKeep, a fast lightweight tool for Illumina and nanopore data that only keeps reads matching the SARSCoV-2 genome. Peak RAM usage is typically below 10MB, and runtime less than one minute. We show that by excluding the polyA tail from the viral reference, ReadItAndKeep prevents bleed-through of human reads, whereas mapping to the human genome lets some reads escape. We believe our test approach (including all possible reads from the human genome, human samples from each of the 26 populations in the 1000 genomes data, and a diverse set of SARSCoV-2 genomes) will also be useful for others.

Bibliographic Details

Martin Hunt; Zamin Iqbal; Jeremy Swann; Bede Constantinides; Philip W. Fowler

Cold Spring Harbor Laboratory

Biochemistry, Genetics and Molecular Biology; Agricultural and Biological Sciences; Immunology and Microbiology; Neuroscience; Pharmacology, Toxicology and Pharmaceutics

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