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SpacePHARER Release 3-5b8c86d
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@milot-mirdita milot-mirdita released this 16 Dec 16:55
· 60 commits to master since this release
3-5b8c86d
5b8c86d
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Learn about vigilant mode.

Changes since Release 2-fc5e668:

New features

  • Perform additional nucl-nucl alignment on protein-search hits to improve precision (turn off by --perform-nucl-aln 0)
  • Add spacer database (Shmakov et al, 2017) to downloaddb
  • Report host LCA per phage if mapping file of hosts to taxonomic identifiers is given
  • Report phage LCA per spacer if mapping file of phages to taxonomic identifiers is given
  • Clean up of command line interface, hide most parameters that are not useful to users
  • Updated base MMseqs2 for additional speedups
  • SpacePHARER runs on more platforms (x86_64+SSE2, ARM64, PPC64LE)

Breaking changes

  • downloadgenome is now called downloaddb

Bugs fixed

  • Fix findpam producing inconsistent output between different strands
  • Speed up combineprotnuclaln and summarizeresults
Assets 9
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