V0.42.1

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