kallisto 0.44.0

kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. On benchmarks with standard RNA-Seq data, kallisto can quantify 30 million human reads in less than 3  minutes on a Mac desktop computer using only the read sequences and a transcriptome index that    itself takes less than 10 minutes to build. Pseudoalignment of reads preserves the key information needed for quantification, and kallisto is therefore not only fast, but also as accurate as existing quantification tools. In fact, because the pseudoalignment procedure is robust to errors in the reads, in many benchmarks kallisto significantly outperforms existing tools.

Accessing the software

To load the module:

$ module load kallisto/0.44.0-iomkl-2018a

An example command to include in your job script:

kallisto index -i transcripts.idx ${KALLISTO_ROOT}/test/transcripts.fasta.gz
kallisto quant -i transcripts.idx -o output -b 100 \
${KALLISTO_ROOT}/test/reads_1.fastq.gz \

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

Previous versions of this application are recorded below:

Known Problems & Limitations


Other Information

The Support Level for this application is An.

Visit the kallisto website for more information regarding this application.

Last modified: 8 June 2018