From 822c464b899656e531f81d88ccb50aba70f4b4b7 Mon Sep 17 00:00:00 2001 From: Hasindu Gamaarachchi Date: Sat, 29 Apr 2023 09:33:27 +1000 Subject: [PATCH] bump version to 1.2 --- README.md | 6 +++--- src/f5c.h | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 9e2ce040..c86e3d6e 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # f5c -An optimised re-implementation of the *index*, *call-methylation* and *eventalign* modules in [Nanopolish](https://github.com/jts/nanopolish). Given a set of basecalled Nanopore reads and the raw signals, *f5c call-methylation* detects the methylated cytosine and *f5c eventalign* aligns raw nanopore signals (events) to the reference k-mers. *f5c* can optionally utilise NVIDIA graphics cards for acceleration. +An optimised re-implementation of the *index*, *call-methylation* and *eventalign* modules in [Nanopolish](https://github.com/jts/nanopolish). Given a set of basecalled Nanopore reads and the raw signals, *f5c call-methylation* detects the methylated cytosine and *f5c eventalign* aligns raw nanopore signals (events) to the reference k-mers. *f5c* can optionally utilise NVIDIA graphics cards for acceleration. f5c v1.2 onwards support the latest nanopore R10.4.1 chemistry. First, the reads have to be indexed using `f5c index`. Then, invoke `f5c call-methylation` to detect methylated cytosine bases. Finally, you may use `f5c meth-freq` to obtain methylation frequencies. Alternatively, invoke `f5c eventalign` to perform event alignment. The results are almost the same as from nanopolish except a few differences due to floating point approximations. @@ -38,7 +38,7 @@ Please cite the following when using *f5c* in your publications: If you are a Linux user and want to quickly try out download the compiled binaries from the [latest release](https://github.com/hasindu2008/f5c/releases). For example: ```sh -VERSION=v1.1 +VERSION=v1.2 wget "https://github.com/hasindu2008/f5c/releases/download/$VERSION/f5c-$VERSION-binaries.tar.gz" && tar xvf f5c-$VERSION-binaries.tar.gz && cd f5c-$VERSION/ ./f5c_x86_64_linux # CPU version ./f5c_x86_64_linux_cuda # cuda supported version @@ -54,7 +54,7 @@ You can also use conda to install *f5c* as `conda install f5c -c bioconda -c con Users are recommended to build from the [latest release](https://github.com/hasindu2008/f5c/releases) tar ball. You need a compiler that supports C++11. Quick example for Ubuntu : ```sh sudo apt-get install libhdf5-dev zlib1g-dev #install HDF5 and zlib development libraries -VERSION=v1.1 +VERSION=v1.2 wget "https://github.com/hasindu2008/f5c/releases/download/$VERSION/f5c-$VERSION-release.tar.gz" && tar xvf f5c-$VERSION-release.tar.gz && cd f5c-$VERSION/ scripts/install-hts.sh # download and compile the htslib ./configure diff --git a/src/f5c.h b/src/f5c.h index cac41db6..0ac5e305 100644 --- a/src/f5c.h +++ b/src/f5c.h @@ -21,7 +21,7 @@ #include #include //required for eventalign -#define F5C_VERSION "1.2-beta" +#define F5C_VERSION "1.2" /******************************* * major hard coded parameters *