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shenwei356 committed Aug 21, 2016
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24 changes: 12 additions & 12 deletions README.md
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# SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation


Documents: [http://shenwei356.github.io/seqkit](http://shenwei356.github.io/seqkit)
Documents: [http://bioinf.shenwei.me/seqkit](http://bioinf.shenwei.me/seqkit)

Source code: [https://github.com/shenwei356/seqkit](https://github.com/shenwei356/seqkit)

Expand All @@ -27,15 +27,15 @@ therefore, it could be easily used in command-line pipe.
## Features

- **Cross-platform** (Linux/Windows/Mac OS X/OpenBSD/FreeBSD,
see [download](http://shenwei356.github.io/seqkit/download/))
see [download](http://bioinf.shenwei.me/seqkit/download/))
- **Light weight and out-of-the-box, no dependencies, no compilation, no configuration**
(see [download](http://shenwei356.github.io/seqkit/download/))
(see [download](http://bioinf.shenwei.me/seqkit/download/))
- **UltraFast** (see [benchmark](/#benchmark)),
**multiple-CPUs supported**.
- **Practical functions supported by 20 subcommands** (see subcommands and
[usage](http://shenwei356.github.io/seqkit/usage/) )
- **Well documented** (detailed [usage](http://shenwei356.github.io/seqkit/usage/)
and [benchmark](http://shenwei356.github.io/seqkit/benchmark/) )
[usage](http://bioinf.shenwei.me/seqkit/usage/) )
- **Well documented** (detailed [usage](http://bioinf.shenwei.me/seqkit/usage/)
and [benchmark](http://bioinf.shenwei.me/seqkit/benchmark/) )
- **Seamlessly parses both FASTA and FASTQ formats**
- **Support STDIN and gziped input/output file, easy being used in pipe**
- **Support custom sequence ID regular expression** (especially useful for searching with ID list)
Expand Down Expand Up @@ -71,13 +71,13 @@ Categories |Features |seqkit |fasta_utilities|fastx_tool
|Reading gzipped file |Yes |Yes |-- |-- |Yes |Yes
|Writing gzip file |Yes |-- |-- |-- |Yes |--

**Note 1**: See [version information](http://shenwei356.github.io/seqkit/benchmark/#softwares) of the softwares.
**Note 1**: See [version information](http://bioinf.shenwei.me/seqkit/benchmark/#softwares) of the softwares.

**Note 2**: See [usage](http://shenwei356.github.io/seqkit/usage/) for detailed options of seqkit.
**Note 2**: See [usage](http://bioinf.shenwei.me/seqkit/usage/) for detailed options of seqkit.

## Installation

Go to [Download Page](http://shenwei356.github.io/seqkit/downlaod) for more download options and changelogs.
Go to [Download Page](http://bioinf.shenwei.me/seqkit/downlaod) for more download options and changelogs.

`seqkit` is implemented in [Golang](https://golang.org/) programming language,
executable binary files **for most popular operating systems** are freely available
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## Usage && Examples

[Usage and examples](http://shenwei356.github.io/seqkit/usage/)
[Usage and examples](http://bioinf.shenwei.me/seqkit/usage/)

[Tutorial](http://shenwei356.github.io/seqkit/tutorial/)
[Tutorial](http://bioinf.shenwei.me/seqkit/tutorial/)

## Benchmark

More details: [http://shenwei356.github.io/seqkit/benchmark/](http://shenwei356.github.io/seqkit/benchmark/)
More details: [http://bioinf.shenwei.me/seqkit/benchmark/](http://bioinf.shenwei.me/seqkit/benchmark/)

Datasets:

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Expand Up @@ -54,7 +54,7 @@ Categories |Features |seqkit |fasta_utilities|fastx_tool
|Reading gzipped file |Yes |Yes |-- |-- |Yes |Yes
|Writing gzip file |Yes |-- |-- |-- |Yes |--

**Note 2**: See [usage](http://shenwei356.github.io/seqkit/usage/) for detailed options of seqkit.
**Note 2**: See [usage](http://bioinf.shenwei.me/seqkit/usage/) for detailed options of seqkit.

## Datasets

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4 changes: 2 additions & 2 deletions doc/docs/usage.md
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Expand Up @@ -103,7 +103,7 @@ Version: 0.3.3
Author: Wei Shen <[email protected]>
Documents : http://shenwei356.github.io/seqkit
Documents : http://bioinf.shenwei.me/seqkit
Source code: https://github.com/shenwei356/seqkit
Usage:
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seqkit replace -p "(.)" -r "\$1 " -s
more on: http://shenwei356.github.io/seqkit/usage/#replace
more on: http://bioinf.shenwei.me/seqkit/usage/#replace
Special repalcement symbols:
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Submodule site updated from b7bdf1 to f7f86e
2 changes: 1 addition & 1 deletion seqkit/cmd/replace.go
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seqkit replace -p "(.)" -r "\$1 " -s
more on: http://shenwei356.github.io/seqkit/usage/#replace
more on: http://bioinf.shenwei.me/seqkit/usage/#replace
Special repalcement symbols:
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