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Phasing out HDF5
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@pmelsted pmelsted released this 12 Feb 23:44
· 824 commits to master since this release
v0.46.2
ae81a86

Phasing out HDF5

For this release HDF5 is not a required dependency for running kallisto bus for single cell RNA-seq analysis. It is still required for compatibility with sleuth and other downstream tools. By default kallisto will not be built with HDF5 support, this can be enabled by running

cmake  .. -DUSE_HDF5=ON

The binaries for this release are compiled with HDF5 built in, but we will switch from using HDF5 in future versions (coordinated with sleuth).

When running kallisto quant without HDF5 support

  • quant without bootstrapping will create the same files as before, except for abundance.h5
  • quant with bootstrapping, -b, will not perform bootstrapping but displays the following warning
    Warning: kallisto was not compiled with HDF5 support so no bootstrapping will be performed. Run quant with --plaintext option or recompile with HDF5 support to obtain bootstrap estimates.
  • quant with -b k and --plaintext will create the bootstrap values in files bs_abundance_i.tsv for i=0..k-1

For users relying on HDF5 support we recommend compiling kallilsto with HDF5 or downloading the kallisto binaries.

Over the next releases HDF5 will gradually be phased out and information on bootstraps will be replaced with a new format.

Changes

  • kallisto pseudo outputs a file of transcript ids
  • Fixes #240
  • kallisto bus allows having sequence split across more than one file, closes #226
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