HIVdb 9.4

Upgrade to HIVdb 9.4 (#884) and fix alignment bugs (#887, #963, #899).

See the milestone for a complete list of changes.

Stitched consensus

The main changes were:

• Added a stitched consensus #745
• Updated to HIVdb 9.0 #686
• Noncoding regions #589
• Launch proviral pipeline #706
• Added chimeric Ghana references for HIVGHA project code #806
• Added concordance evaluation #821

For the full list of issues, see the milestone.

Note: v7.15.12 is only a change to the MiCall watcher to suspend the proviral upload into QAI, as it is currently failing.
v7.15.13 pins merge-mates to the commit that I used to test v7.15 (there have since been new commits that break our code)

To do when putting the new release in place:

• Add Charlotte to email recipients
• Add a new sample to the list of samples to test: 90906A-HCV_S122 from run 16-Oct-2020.M01841

Primers by project

The main change is to choose a set of primers to trim, issue #625. See the milestone for a list of other issues.

SARS-CoV-2 support

The main feature of this release is #549 to add SARS-CoV-2 reference sequences.

Other changes:

• #536 upgrade HIVdb to 8.9-1
• #584 and #585 make it easier to start using docker version
• #480 and #583 improve genome coverage plots
• #530 filter primer dimers

See the milestone for a complete list.

De novo assembly

The big change is #442, adding a de novo assembly method to the standard remapping method.

Also included:

• #486 a project region for GP120, and report V3LOOP coverage with G2P alignments while GP120 reports coverage from remapped or assembled reads.
• #524 Insertion counts are wrong.
• #471 and #473 improve efficiency of micall_watcher script.

See the milestone for a complete list.

De novo assembly (preview)

Development preview of #442 de novo assembly.

HCV subtype bug

Fixes two bugs related to HCV subtypes: #470 and #472.

Container Runs

The main improvements in this release are in the MiCall watcher, specifically changing to Kive's new container runs (#460). Related fixes are #458 and #459.

• Update HIVdb to 8.8 (#448).
• Some bugs when combining MIDI and whole genome samples: #469, #468, #465, #463, #462, #454, and #450.

For the complete list of issues, see the milestone.

Configuration changes:

• Convert old Kive runs to container runs.
• Upload pipeline definitions to QAI for #441.
• Remove bowtie2 from Kive's host system, because it interferes with the version inside the Singularity container.
• Update kiveapi to 0.12.

HCV Reports

Add HCV reports (#412), then update HCV resistance rules (#436).

• Combine whole-genome and MidHCV samples to get complete coverage in HCV reports (#427 and #438).
• Fix a couple of bugs in the consensus sequences (#417 and #420).
• Add more details to resistance results (#445).
• Fix external datasets (#452).
• Error handling in micall_watcher (#449, #451, and #453).

For the full list of changes, see the milestone.

Mutation Prevalance

Add prevalence of mutations to MiCall reports (#402), as well as other report changes (#407 and #408). Other changes:

• #409 and #393 reduce memory consumption
• #414 rename G2P overlap to V3 overlap
• #413 add seed for HIV-B-Consensus