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fix snakeprofile stuff

Status: Open.

#114 In vdblab/vdblab-shotgun;

· miraep8 opened on Feb 10, 2026

remove hardcoded versions from mpa output files

Status: Open.

#112 In vdblab/vdblab-shotgun;

· nickp60 opened on Nov 13, 2025

Maybe tone down or better scale annotation sharding?

Status: Open.

#110 In vdblab/vdblab-shotgun;

· miraep8 opened on Sep 29, 2025

move strainphlan logic to separate repo

needed-for-0.5.0

Status: Open.

#107 In vdblab/vdblab-shotgun;

· nickp60 opened on Apr 18, 2025

Add MGEfinder?

Status: Open.

#106 In vdblab/vdblab-shotgun;

· miraep8 opened on Apr 16, 2025

Fix seed in downsampling

Status: Open.

#104 In vdblab/vdblab-shotgun;

· nickp60 opened on Mar 13, 2025

Update the host removal with some improved tools?

Status: Open.

#103 In vdblab/vdblab-shotgun;

· miraep8 opened on Mar 11, 2025

Compress kraken2.out files?

good first issueGood for newcomersGood for newcomers

needed-for-0.5.0

Status: Open.

#94 In vdblab/vdblab-shotgun;

· miraep8 opened on Sep 23, 2024

Clean up the temporary annotation outputs

good first issueGood for newcomersGood for newcomers

Status: Open.

#93 In vdblab/vdblab-shotgun;

· miraep8 opened on Sep 23, 2024

Trimming: parameter tuning?

Status: Open.

#92 In vdblab/vdblab-shotgun;

· miraep8 opened on Sep 16, 2024

Host read removal: use human pangenome reference

Status: Open.

#89 In vdblab/vdblab-shotgun;

· funnell opened on May 21, 2024

Can we parse the kmer output of fastqc to estimate de-duplication memory requirements?

Status: Open.

#87 In vdblab/vdblab-shotgun;

· nickp60 opened on May 20, 2024