From ead580317cb5cdc163acc7fcaff55368a51a29ff Mon Sep 17 00:00:00 2001 From: Lior Pachter Date: Sun, 14 Jul 2019 17:14:55 -0700 Subject: [PATCH] Update README.md --- README.md | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 23e6c8b3..8205fc6a 100644 --- a/README.md +++ b/README.md @@ -7,9 +7,9 @@ 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 bulk RNA-seq 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 +itself takes 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 than existing +is therefore not only fast, but also comparably accurate to other existing quantification tools. In fact, because the pseudoalignment procedure is robust to errors in the reads, in many benchmarks __kallisto__ significantly outperforms existing tools. The __kallisto__ algorithms are described in more detail in: @@ -18,7 +18,7 @@ NL Bray, H Pimentel, P Melsted and L Pachter, [Near optimal probabilistic RNA-se Scripts reproducing all the results of the paper are available [here](https://github.com/pachterlab/kallisto_paper_analysis). -__kallisto__ quantified RNA-Seq can be analyzed with [__sleuth__](https://github.com/pachterlab/sleuth/). +__kallisto__ quantified bulk RNA-Seq can be analyzed with [__sleuth__](https://github.com/pachterlab/sleuth/). __kallisto__ can be used together with [__bustools__](https://bustools.github.io/) to pre-process single-cell RNA-seq data. See the [kallistobus.tools](https://www.kallistobus.tools/) website for instructions. @@ -28,7 +28,7 @@ Please visit http://pachterlab.github.io/kallisto/manual.html for the manual. ## License -Please read the license before using kallisto. The license is distributed with __kallisto__ in the file `license.txt` also viewable [here](https://pachterlab.github.io/kallisto/download). +__kallisto__ is distributed under the BSD-2 license. The license is distributed with __kallisto__ in the file `license.txt`, which is also viewable [here](https://pachterlab.github.io/kallisto/download). Please read the license before using __kallisto__. ## Getting help @@ -36,8 +36,7 @@ For help running __kallisto__, please post to the [kallisto-and-applications Goo ## Reporting bugs -Please report bugs to the [Github issues -page](https://github.com/pachterlab/kallisto/issues) +Please report bugs to the [Github issues page](https://github.com/pachterlab/kallisto/issues) ## Development and pull requests