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Published April 11, 2023 | Version v0.7.0
Software Open

pangenome/smoothxg: smoothxg 0.7.0 - Deduplicato

Creators

  • 1. The University of Tennessee Health Science Center (@uthsc)
  • 2. University of Tennessee Health Science Center (UTHSC)
  • 3. QBiC
  • 4. @UCSantaCruzComputationalGenomicsLab
  • 5. Arenaria
  • 6. University of California Santa Cruz Genomics Institute
  • 7. University of Tenneseee

Description

Buildable Source Tarball: smoothxg-v0.7.0.tar.gz

The main power-up in this version is the execution of partial order alignment (POA) on unique sequences by duplicating the POA blocks before their alignment. On average, the runtime improvement is around 5X with SPOA and abPOA; on nasty POA blocks, it can be >100X faster than before with SPOA.

This introduces:

  • allow writing FASTAs of only hard blocks #181 by @AndreaGuarracino
  • Perform the POA on unique sequences + Emit POA blocks information in a table #183 by @AndreaGuarracino
  • Fix versioning #186 by @AndreaGuarracino
  • updated odgi with inject, paths, flip, overlap, and sort fixings #185 #187 #188 by @AndreaGuarracino

Files

pangenome/smoothxg-v0.7.0.zip

Files (205.2 kB)

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md5:e75fdf4afe7a1f8b442acc393cb2fa1e
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Additional details

Related works

Is supplement to
https://github.com/pangenome/smoothxg/tree/v0.7.0 (URL)