kallisto is a program for quantifying abundances of transcripts from RNASeq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.
kallisto is described in detail in:
  • Nicolas L Bray, Harold Pimentel, Páll Melsted and Lior Pachter, Near-optimal probabilistic RNA-seq quantification, Nature Biotechnology 34, 525–527 (2016), doi:10.1038/nbt.3519