Centralize sequence read operations #3237

Job	Run time
check-docs	42s
mypy	1m 0s
pathogen-repo-ci-v0 (avian-flu)	52s
pathogen-repo-ci (dengue)	2m 56s
pathogen-repo-ci-v0 (ebola)	1m 1s
pathogen-repo-ci (lassa)	7m 53s
pyright	19s
pathogen-repo-ci-v0 (mumps)	56s
pathogen-repo-ci (measles)	1m 21s
pathogen-repo-ci-v0 (ncov)	1m 3s
pathogen-repo-ci (mpox)	1m 15s
pathogen-repo-ci-v0 (rsv)	8m 41s
test (python=3.9 biopython=1.80)	13m 2s
pathogen-repo-ci (oropouche)	1m 29s
pathogen-repo-ci-v0 (seasonal-flu)	1m 17s
pathogen-repo-ci (rabies)	2m 33s
test (python=3.9 biopython=1.82)	13m 19s
pathogen-repo-ci-v0 (tb)	1m 15s
pathogen-repo-ci (seasonal-cov)	1m 28s
test (python=3.9 biopython=latest)	13m 21s
pathogen-repo-ci (wnv)	1m 1s
test (python=3.10 biopython=1.80)	14m 18s
pathogen-repo-ci (yellow-fever)	4m 20s
test (python=3.10 biopython=1.82)	13m 36s
pathogen-repo-ci (zika)	1m 3s
test (python=3.10 biopython=latest)	13m 40s
test (python=3.11 biopython=1.80)	13m 43s
test (python=3.11 biopython=1.82)	13m 35s
test (python=3.11 biopython=latest)	13m 40s
test (python=3.12 biopython=1.82)	21m 26s
test (python=3.12 biopython=latest)	21m 18s
build-docs / build	2m 31s
codecov	13s
release	0s
rebuild-docker-image	0s
	3h 30m 7s

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