Centralize sequence read operations #3213

Job	Run time
check-docs	39s
pathogen-repo-ci (dengue)	2m 52s
mypy	57s
pathogen-repo-ci-v0 (avian-flu)	1m 4s
pathogen-repo-ci (lassa)	7m 48s
pathogen-repo-ci-v0 (ebola)	1m 7s
pathogen-repo-ci (measles)	1m 22s
pyright	12s
pathogen-repo-ci (mpox)	1m 13s
pathogen-repo-ci-v0 (mumps)	53s
test (python=3.9 biopython=1.80)	12m 51s
pathogen-repo-ci (oropouche)	1m 23s
pathogen-repo-ci-v0 (ncov)	1m 4s
test (python=3.9 biopython=1.82)	13m 27s
pathogen-repo-ci (rabies)	2m 16s
pathogen-repo-ci-v0 (rsv)	8m 27s
test (python=3.9 biopython=latest)	13m 12s
pathogen-repo-ci (seasonal-cov)	1m 26s
pathogen-repo-ci-v0 (seasonal-flu)	1m 17s
test (python=3.10 biopython=1.80)	14m 8s
pathogen-repo-ci (wnv)	1m 1s
pathogen-repo-ci-v0 (tb)	1m 18s
test (python=3.10 biopython=1.82)	13m 27s
pathogen-repo-ci (yellow-fever)	4m 19s
test (python=3.10 biopython=latest)	13m 51s
pathogen-repo-ci (zika)	1m 5s
test (python=3.11 biopython=1.80)	13m 15s
test (python=3.11 biopython=1.82)	13m 27s
test (python=3.11 biopython=latest)	13m 31s
test (python=3.12 biopython=1.82)	13m 30s
test (python=3.12 biopython=latest)	13m 30s
build-docs / build	2m 16s
codecov	0s
release	0s
rebuild-docker-image	0s
	3h 12m 8s

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