npm

kallisto

Quantify transcript abundances from RNA-Seq data using k-mer matching

brewmacoslinux

Try with needOr install directly

Source

About

Quantify abundances of transcripts from RNA-Seq data

Commands

kallisto

Examples

Build a kallisto index from a reference transcriptome$ kallisto index -i transcripts.idx transcripts.fasta

Quantify abundances for paired-end RNA-Seq reads$ kallisto quant -i transcripts.idx -o output reads_1.fastq reads_2.fastq

Quantify single-end reads with bootstrap sampling for uncertainty estimation$ kallisto quant -i transcripts.idx -o output --single -l 200 -s 20 -b 100 reads.fastq