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artic-network / fieldbioinformatics

The ARTIC field bioinformatics pipeline
MIT License
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Enforce amplicon coverage #61

Closed will-rowe closed 3 years ago

will-rowe commented 3 years ago

This PR updates align_trim so that alignment segments not spanning an entire amplicon are dropped.

This PR should be considered after https://github.com/artic-network/fieldbioinformatics/pull/60

Although Travis tests pass, the test dataset NRW01 (not run by Travis) will currently fail due to the consensus sequence produced by this PR containing extra terminal Ns. This is due to low coverage in the final amplicon, which causes a larger depth mask than previously had for this sample. We can either update the consensus sequence for NRW01 tests or play with the minimum coverage in artic_make_depth_mask

Old coverage mask for NRW01:

MN908947.3  1   54
MN908947.3  29810   29903

New coverage mask for NRW01:

MN908947.3  1   54
MN908947.3  29666   29903
will-rowe commented 3 years ago

Closing as this is outdated. I will add a new PR for full-length alignments later.