kallisto specifications


Unique identifier OMICS_08418
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input format FASTQ
Operating system Mac OS, Windows
Computer skills Advanced
Version 0.42.1
Stability Stable
Maintained Yes



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  • person_outline Cyril Zipfel <>

kallisto article

kallisto citations

PMCID: 5818608

[…] coming from this part over all reads (expected count), the transcripts per million (tpm), and fragments per kilobase of transcript per million mapped reads (fpkm), were calculated using rsem70 and kallisto71. a relative expression level of each viral gene was measured using the fpkm value of one gene divided by the fpkm value of the highest expressed gene of the same virus., 1/10 and 1/20 […]

PMCID: 5799185

[…] assembly completeness using busco29 and recovered 90% complete or partial alignments of 3950 mammalian orthologs. all sequence data have been uploaded to genbank (bioproject id prjna399240). we used kallisto30 to estimate abundance and deseq231 to call differential expression. in total, 1,871 transcripts were differentially expressed between pregnant and non-pregnant animals (fdr-adjusted p <  […]

PMCID: 5614841

[…] truseq mrna library prep kit, and sequenced on illumina hiseq 2500 and/or hiseq 4000 platform., strand-specific single-end rna-seq read files were analyzed to obtain transcript level counts using kallisto66, with the settings –rf-stranded -b 100. the counts were subsequently passed to the tximport r package to collapse to gene level counts. pairwise differential expression analysis […]

PMCID: 5600148

[…] a scaling factor per condition. differences across condition for the different methods’ quantifications were tested using a t-test of log2 (tpm + 1)., all tests were performed with express v1.5.1, kallisto v0.43.0, salmon v0.8.0 and bowtie2 v2.2.4. reads were aligned with bowtie2 using the parameters --no-discordant -k 200, and -p to set the number of threads. on the rsem-sim data, […]

PMCID: 5301240

[…] and its receptors adipor1 and adipor2, pparg coactivator 1 alpha, mtor and ppara, among others., in silico transcript abundance quantification was conducted using the ultrafast quasi-alignment tool kallisto, which pseudoaligned 94.45 ± 0.64% of sequencing reads from each sample to the assembly. differential gene expression analysis was conducted at the gene level using deseq2, selecting […]

kallisto institution(s)
Department of Cell and Developmental Biology, John Innes Centre, Norwich, UK; The Sainsbury Laboratory, Norwich, UK

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