ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads
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 f...
| المؤلفون الرئيسيون: | , , , , |
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| التنسيق: | Journal article |
| اللغة: | English |
| منشور في: |
Oxford University Press
2022
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| _version_ | 1826308263037108224 |
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| author | Hunt, M Swann, J Constantinides, B Fowler, PW Iqbal, Z |
| author_facet | Hunt, M Swann, J Constantinides, B Fowler, PW Iqbal, Z |
| author_sort | Hunt, M |
| collection | OXFORD |
| description | 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. |
| first_indexed | 2024-03-07T07:16:57Z |
| format | Journal article |
| id | oxford-uuid:83e55d1b-6b4b-40d9-af19-bd06093cbce0 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T07:16:57Z |
| publishDate | 2022 |
| publisher | Oxford University Press |
| record_format | dspace |
| spelling | oxford-uuid:83e55d1b-6b4b-40d9-af19-bd06093cbce02022-08-16T11:47:04ZReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing readsJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:83e55d1b-6b4b-40d9-af19-bd06093cbce0EnglishSymplectic ElementsOxford University Press2022Hunt, MSwann, JConstantinides, BFowler, PWIqbal, ZViral 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. |
| spellingShingle | Hunt, M Swann, J Constantinides, B Fowler, PW Iqbal, Z ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads |
| title | ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads |
| title_full | ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads |
| title_fullStr | ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads |
| title_full_unstemmed | ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads |
| title_short | ReadItAndKeep: rapid decontamination of SARS-CoV-2 sequencing reads |
| title_sort | readitandkeep rapid decontamination of sars cov 2 sequencing reads |
| work_keys_str_mv | AT huntm readitandkeeprapiddecontaminationofsarscov2sequencingreads AT swannj readitandkeeprapiddecontaminationofsarscov2sequencingreads AT constantinidesb readitandkeeprapiddecontaminationofsarscov2sequencingreads AT fowlerpw readitandkeeprapiddecontaminationofsarscov2sequencingreads AT iqbalz readitandkeeprapiddecontaminationofsarscov2sequencingreads |