https://github.com/pachterlab/kallisto

Near-optimal RNA-Seq quantification
https://github.com/pachterlab/kallisto

kallisto pseudoalignment rna-seq

Last synced: 3 months ago
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Near-optimal RNA-Seq quantification

• Host: GitHub
• URL: https://github.com/pachterlab/kallisto
• Owner: pachterlab
• License: bsd-2-clause
• Created: 2014-11-13T00:27:48.000Z (almost 10 years ago)
• Default Branch: master
• Last Pushed: 2024-07-26T18:32:34.000Z (3 months ago)
• Last Synced: 2024-07-26T20:28:34.831Z (3 months ago)
• Topics: kallisto, pseudoalignment, rna-seq
• Language: C
• Homepage: https://pachterlab.github.io/kallisto
• Size: 9.39 MB
• Stars: 637
• Watchers: 47
• Forks: 168
• Open Issues: 174
• Metadata Files:
  • Readme: README.md
  • License: license.txt

Awesome Lists containing this project

• awesome-single-cell - kallisto - [C++] - kallisto is a program for quantifying abundances of transcripts or genes from bulk or single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. (Software packages / RNA-seq)

README

        
# kallisto

__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 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 than 10 minutes to build. Pseudoalignment of reads

preserves the key information needed for quantification, and __kallisto__

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:

NL Bray, H Pimentel, P Melsted and L Pachter, [Near optimal probabilistic RNA-seq quantification](http://www.nature.com/nbt/journal/v34/n5/abs/nbt.3519.html), Nature Biotechnology __34__, p 525--527 (2016).

Scripts reproducing all the results of the paper are available [here](https://github.com/pachterlab/kallisto_paper_analysis).

__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.

## Manual

Please visit http://pachterlab.github.io/kallisto/manual.html for the manual.

## License

__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

For help running __kallisto__, please post to the [kallisto-and-applications Google Group](https://groups.google.com/forum/#!forum/kallisto-and-applications).

## Reporting bugs

Please report bugs to the [Github issues page](https://github.com/pachterlab/kallisto/issues)

## Development and pull requests

We typically develop on separate branches, then merge into devel once features

have been sufficiently tested. `devel` is the latest, stable, development

branch. `master` is used only for official releases and is considered to be

stable. If you submit a pull request (thanks!) please make sure to request to

merge into `devel` and NOT `master`. Merges usually only go into `master`, but

not out.