Bias modeling, pseudobam output, and threaded bootstraps

[Harold Pimentel]

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.

The Linux binary is currently unavailable, but once static linking has been resolved, we will post it.

Thanks,

Harold