Selected article for: "host genome and International license"
Author: Gage Kahl Moreno; Katarina M Braun; Peter J Halfmann; Trent M Prall; Kasen K Riemersma; Amelia K Haj; Joseph Lalli; Kelsey R Florek; Thomas C Friedrich; Yoshihiro Kawaoka; David H O'Connor
Title: Limited SARS-CoV-2 diversity within hosts and following passage in cell culture
  • Document date: 2020_4_20
    • ID: izu5x2d4_11
    Snippet: Seventy-two hours after sequencing was initiated, raw sequencing reads were demultiplexed 351 using qcat (https://github.com/nanoporetech/qcat). In order to deplete host sequences, 352 sequencing reads are mapped against host genome and transcript references, and unmapped 353 reads are saved. Reads were then trimmed by 30bp on each side to discard SISPA primer 354 sequences. In this step, reads with quality scores ≤ 7 were discarded. Cleaned vi.....
    Document: Seventy-two hours after sequencing was initiated, raw sequencing reads were demultiplexed 351 using qcat (https://github.com/nanoporetech/qcat). In order to deplete host sequences, 352 sequencing reads are mapped against host genome and transcript references, and unmapped 353 reads are saved. Reads were then trimmed by 30bp on each side to discard SISPA primer 354 sequences. In this step, reads with quality scores ≤ 7 were discarded. Cleaned viral reads were 355 then mapped to the severe acute respiratory syndrome coronavirus 2 isolate 2019-nCoV/USA-356 WI1/2020 consensus sequence (Genbank: MT039887.1, originally sequenced by the CDC) 357 using minimap2. Minor variants from ONT sequences that comprise at least 10% of total 358 sequences in any of the samples were identified using the bbmap callvariants.sh tool 359 . CC-BY 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.20.051011 doi: bioRxiv preprint (https://jgi.doe.gov/data-and-tools/bbtools/). The entire ONT analysis pipeline is available at this 360 GitHib address https://github.com/katarinabraun/SARSCoV2_passage_MS. 361

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