Tool: Hera-T: an efficient and accurate algorithm for single-cell transcript quantification
gravatar for Jennifer Pham
6 months ago by
Jennifer Pham290
San Diego CA
Jennifer Pham290 wrote:

We are delighted to introduce hera-T, a fast and accurate algorithm to quantify gene abundances from 10X-Chromium data with high rates of non-exonic reads, developed by BioTuring team.

hera-T devises a new strategy for aligning reads to both transcriptome and genome references that considerably reduces both the running time and memory consumption. For a single-cell data set with 49M reads, hera-T took only 1.75 minutes to process and consumed 8GB RAM. For a sample dataset of 11 billion reads (about 1.3 million cells), hera-T needs 24GB RAM and takes 4 hours to finish.

enter image description here

The t-SNE plots from hera-T and CellRanger are almost indistinguishable. Minor differences come from some difficult splicing alignment scenarios (with short exons) that hera-T addresses but Cell Ranger fails to address. ( enter image description here

Please find some initial benchmarks of hera-T here.

To get hera-T package, please contact us at

ADD COMMENTlink written 6 months ago by Jennifer Pham290
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1913 users visited in the last hour