12 May 2015

This is version 0.42.1 of Kallisto. We recommend that users upgrade to this version.

Updates include

  • index
    • now accepts multiple FASTA files and creates an index of all the targets
    • clips the polyA tail of transcripts that end with runs of A of length 10 or greater
  • quant
    • now accepts multiple FASTQ paired-end files, or single-end files
    • --single flag to specify single-end reads
    • simplifies jumping rules
    • uses soft-intersect, if one read has no mapping k-mers the other end is used for pseudoalignment
    • outputs number of reads processed and number of reads pseudoaligned