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update readme
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hasindu2008 committed Mar 2, 2023
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5 changes: 4 additions & 1 deletion README.md
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Expand Up @@ -33,6 +33,7 @@ Please cite the following in your publications when using *slow5lib/pyslow5*:

## Building

Building slow5lib requires a compiler that supports C99 standard (with X/Open 7 POSIX 2008 extensions), which is widely available.
To build the C/C++ library :

```sh
Expand Down Expand Up @@ -115,6 +116,9 @@ You can invoke `examples/build.sh` to compile the example programmes. Have a loo
Python wrapper for slow5lib or *pyslow5* can be installed using conda as `conda install pyslow5 -c bioconda -c conda-forge` or pypi as `pip install pyslow5`.
The instructions to build *pyslow5* and the usage instructions are [here](https://hasindu2008.github.io/slow5lib/pyslow5_api/pyslow5.html).

### Other languages

A slow5 library for RUST programming language developed by [@bsaintjo](https://github.com/bsaintjo/) is available [here](https://docs.rs/slow5/latest/slow5). A slow5 library in GO language developed by [@Koeng101](https://github.com/Koeng101) is available [here](https://github.com/TimothyStiles/poly/pull/220). We are highly grateful to these community efforts. If anyone is interested in a library form another language, feel free to open an issue.

### Current limitations & future work

Expand All @@ -130,6 +134,5 @@ slow5lib is a reference implementation for SLOW5 format. Depending on the intere

*slow5lib* from version 0.3.0 onwards has built in [StreamVByte](https://github.com/lemire/streamvbyte) compression support to enable even smaller file sizes, which is applied to the raw signal by default when producing BLOW5 files. *zlib* compression is then applied by default to each SLOW5 record. If *zstd* is used instead of *zlib* on top of *StreamVByte*, it is similar to ONT's latest [vbz](https://github.com/nanoporetech/vbz_compression) compression. BLOW5 files with *zstd+StreamVByte* are still about 25% smaller than vbz compressed FAST5 files.


## Acknowledgement
slow5lib uses [klib](https://github.com/attractivechaos/klib) and [StreamVByte](https://github.com/lemire/streamvbyte). Some code snippets have been taken from [Minimap2](https://github.com/lh3/minimap2) and [Samtools](http://samtools.sourceforge.net/).
6 changes: 4 additions & 2 deletions docs/getting_started.md
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Expand Up @@ -27,7 +27,7 @@ Please cite the following in your publications when using *slow5lib/pyslow5*:

## Building

To build the C/C++ library :
Building slow5lib requires a compiler that supports C99 standard (with X/Open 7 POSIX 2008 extensions), which is widely available. To build the C/C++ library :

```sh
sudo apt-get install zlib1g-dev #install zlib development libraries
Expand All @@ -45,7 +45,6 @@ On Fedora/CentOS : sudo dnf/yum install zlib-devel
On OS X : brew install zlib
```


#### Optional zstd compression

You can optionally enable [*zstd* compression](https://facebook.github.io/zstd) support when building *slow5lib* by invoking `make zstd=1`. This requires __zstd 1.3 or higher development libraries__ installed on your system:
Expand Down Expand Up @@ -109,6 +108,9 @@ You can invoke `examples/build.sh` to compile the example programmes. Have a loo
Python wrapper for slow5lib or *pyslow5* can be installed using conda as `conda install pyslow5 -c bioconda -c conda-forge` or pypi as `pip install pyslow5`.
The instructions to build *pyslow5* and the usage instructions are [here](https://hasindu2008.github.io/slow5lib/pyslow5_api/pyslow5.html).

### Other languages

A slow5 library for RUST programming language developed by [@bsaintjo](https://github.com/bsaintjo/) is available [here](https://docs.rs/slow5/latest/slow5). A slow5 library in GO language developed by [@Koeng101](https://github.com/Koeng101) is available [here](https://github.com/TimothyStiles/poly/pull/220). We are highly grateful to these community efforts. If anyone is interested in a library form another language, feel free to open an issue.

### Current limitations & future work

Expand Down

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