Journal article
ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads
- Abstract:
- Viral sequence data from clinical samples frequently contain contaminating human reads, 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 SARS-CoV-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 SARS-CoV-2 genomes) will also be useful for others.
- Publication status:
- Published
- Peer review status:
- Peer reviewed
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(Preview, Version of record, pdf, 189.6KB, Terms of use)
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- Publisher copy:
- 10.1093/bioinformatics/btac311
Authors
- Publisher:
- Oxford University Press
- Journal:
- Bioinformatics More from this journal
- Volume:
- 38
- Issue:
- 12
- Pages:
- 3291–3293
- Publication date:
- 2022-05-13
- Acceptance date:
- 2022-05-02
- DOI:
- EISSN:
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1460-2059
- ISSN:
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1367-4803
- Language:
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English
- Keywords:
- Pubs id:
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1259374
- Local pid:
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pubs:1259374
- Deposit date:
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2022-05-13
- ARK identifier:
Terms of use
- Copyright holder:
- Hunt et al.
- Copyright date:
- 2022
- Rights statement:
- ©2022 The Author(s). Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
- Licence:
- CC Attribution (CC BY)
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