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https://github.com/yijunyu/fastseq

Last synced: 10 days ago
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Host: GitHub
URL: https://github.com/yijunyu/fastseq
Owner: yijunyu
Created: 2020-05-17T20:23:37.000Z (over 4 years ago)
Default Branch: master
Last Pushed: 2020-06-10T08:25:07.000Z (over 4 years ago)
Last Synced: 2024-11-06T03:46:23.570Z (about 2 months ago)
Language: ANTLR
Size: 509 MB
Stars: 0
Watchers: 2
Forks: 1
Open Issues: 0
Metadata Files:
- Readme: README.md

Awesome Lists containing this project

README

        # fastSeq - a faster genome sequencing toolkit

[![Open in Gitpod](https://gitpod.io/button/open-in-gitpod.svg)](https://gitpod.io/#https://github.com/yijunyu/fastseq)

You can also run it using the following docker command:

```bash

docker run -it yijun/nucleus

```

## Dependencies

* https://github.com/google/protobuf

* https://github.com/google/clif

* https://github.com/google/nucleus

* https://github.com/google/deepvariant

## Usage

```bash

cd /home/gitpod/fastseq/nucleus

bazel build -c opt $COPT_FLAGS nucleus/examples:all

```

## References

[1] Yijun Yu. "[fAST: Flattening Abstract Syntax Trees for Efficiency](http://oro.open.ac.uk/59268/)". In: 41st ACM/IEEE International Conference on Software Engineering, 25-31 May 2019, Montreal, Canada, ACM and IEEE.

[demo](https://gitpod.io/#https://github.com/yijunyu/demo), [paper](http://oro.open.ac.uk/59268), [poster](doc/fast-poster-A0.pdf)