Centralize sequence read operations #3220

Job	Run time
mypy	53s
pathogen-repo-ci (dengue)	2m 56s
pathogen-repo-ci-v0 (avian-flu)	53s
pathogen-repo-ci (lassa)	7m 41s
pyright	15s
pathogen-repo-ci-v0 (ebola)	53s
pathogen-repo-ci (measles)	1m 23s
pathogen-repo-ci-v0 (mumps)	1m 12s
pathogen-repo-ci (mpox)	1m 26s
pathogen-repo-ci-v0 (ncov)	1m 3s
pathogen-repo-ci (oropouche)	1m 28s
check-docs	44s
pathogen-repo-ci-v0 (rsv)	9m 15s
pathogen-repo-ci (rabies)	3m 30s
test (python=3.9 biopython=1.80)	13m 45s
pathogen-repo-ci-v0 (seasonal-flu)	1m 21s
pathogen-repo-ci (seasonal-cov)	1m 26s
pathogen-repo-ci-v0 (tb)	1m 16s
pathogen-repo-ci (wnv)	1m 7s
pathogen-repo-ci (yellow-fever)	4m 22s
test (python=3.9 biopython=1.82)	14m 21s
test (python=3.9 biopython=latest)	13m 16s
pathogen-repo-ci (zika)	59s
test (python=3.10 biopython=1.80)	13m 40s
test (python=3.10 biopython=1.82)	13m 27s
test (python=3.10 biopython=latest)	13m 33s
test (python=3.11 biopython=1.80)	13m 43s
test (python=3.11 biopython=1.82)	13m 28s
test (python=3.11 biopython=latest)	13m 12s
test (python=3.12 biopython=1.82)	20m 36s
test (python=3.12 biopython=latest)	20m 45s
build-docs / build	2m 18s
codecov	14s
release	0s
rebuild-docker-image	0s
	3h 30m 21s

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