Centralize sequence read operations #3200

Job	Run time
check-docs	42s
mypy	58s
pathogen-repo-ci (dengue)	2m 40s
pathogen-repo-ci-v0 (avian-flu)	59s
pathogen-repo-ci (lassa)	7m 19s
pathogen-repo-ci-v0 (ebola)	1m 2s
pathogen-repo-ci (measles)	1m 18s
pyright	19s
pathogen-repo-ci-v0 (mumps)	1m 3s
test (python=3.9 biopython=1.80)	13m 12s
pathogen-repo-ci-v0 (ncov)	1m 3s
test (python=3.9 biopython=1.82)	13m 11s
pathogen-repo-ci-v0 (rsv)	8m 53s
test (python=3.9 biopython=latest)	13m 20s
pathogen-repo-ci (mpox)	1m 13s
pathogen-repo-ci-v0 (seasonal-flu)	1m 17s
test (python=3.10 biopython=1.80)	13m 22s
pathogen-repo-ci (oropouche)	1m 22s
pathogen-repo-ci-v0 (tb)	1m 16s
test (python=3.10 biopython=1.82)	13m 11s
pathogen-repo-ci (rabies)	2m 23s
test (python=3.10 biopython=latest)	13m 38s
pathogen-repo-ci (seasonal-cov)	1m 29s
test (python=3.11 biopython=1.80)	13m 20s
pathogen-repo-ci (wnv)	1m 15s
test (python=3.11 biopython=1.82)	13m 15s
pathogen-repo-ci (yellow-fever)	4m 20s
test (python=3.11 biopython=latest)	13m 38s
pathogen-repo-ci (zika)	1m 7s
test (python=3.12 biopython=1.82)	13m 38s
test (python=3.12 biopython=latest)	13m 38s
build-docs / build	2m 57s
codecov	0s
release	0s
rebuild-docker-image	0s
	3h 12m 18s

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