09 June 2015

This is version 0.42.2 of Kallisto.

Updates include

  • index
    • the index has been updated to include more of the transcript information
    • indices should be slightly smaller than before
    • indices constructed with previous versions will not work with this version, rerun your index command
  • quant
    • Bootstraps can be run in multithreaded mode, use option -t to specify number of threads
    • If only one read of a paired end maps, kallisto will check the transcript positions to discard reads that would go outside of transcript given the mean fragment length.
    • Pseudobam. Pseudoalignments can now be output in SAM format to standard output. For more details on the output see pseudobam
    • Sequence specific bias. kallisto can learn a model for sequence specific bias and correct the abundances accordingly.
    • TSV. All output text files have been changed to .tsv ending.