Centralize sequence read operations #3209

Job	Run time
check-docs	42s
mypy	57s
pathogen-repo-ci (dengue)	3m 27s
pathogen-repo-ci (lassa)	8m 13s
pathogen-repo-ci-v0 (avian-flu)	1m 27s
pathogen-repo-ci (measles)	2m 5s
pathogen-repo-ci-v0 (ebola)	1m 31s
pyright	13s
pathogen-repo-ci (mpox)	1m 49s
pathogen-repo-ci-v0 (mumps)	1m 33s
pathogen-repo-ci (oropouche)	1m 58s
pathogen-repo-ci-v0 (ncov)	1m 32s
pathogen-repo-ci (rabies)	2m 52s
pathogen-repo-ci-v0 (rsv)	9m 44s
pathogen-repo-ci (seasonal-cov)	2m 1s
test (python=3.9 biopython=1.80)	12m 53s
pathogen-repo-ci (wnv)	1m 36s
test (python=3.9 biopython=1.82)	12m 53s
test (python=3.9 biopython=latest)	13m 11s
pathogen-repo-ci (yellow-fever)	4m 50s
pathogen-repo-ci-v0 (seasonal-flu)	1m 44s
test (python=3.10 biopython=1.80)	13m 39s
pathogen-repo-ci (zika)	1m 33s
pathogen-repo-ci-v0 (tb)	1m 51s
test (python=3.10 biopython=1.82)	13m 48s
test (python=3.10 biopython=latest)	13m 38s
test (python=3.11 biopython=1.80)	13m 27s
test (python=3.11 biopython=1.82)	13m 53s
test (python=3.11 biopython=latest)	13m 51s
test (python=3.12 biopython=1.82)	13m 13s
test (python=3.12 biopython=latest)	13m 38s
build-docs / build	2m 18s
codecov	0s
release	0s
rebuild-docker-image	0s
	3h 22m 0s

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