From 09534069c804c8c9b4034353cbe74d86a447e576 Mon Sep 17 00:00:00 2001 From: Andrea Cracco Date: Mon, 4 Nov 2024 10:58:19 +0200 Subject: [PATCH] Update README --- README.md | 25 ++++++++++++++++++------- 1 file changed, 18 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 3cba4c2..b320e21 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,20 @@ +[![BioConda Install](https://img.shields.io/conda/dn/bioconda/ggcat.svg?style=flag&label=BioConda%20install)](https://anaconda.org/bioconda/ggcat) +[![License](https://img.shields.io/github/license/algbio/ggcat)](https://mit-license.org/) +[![GitHub release (latest by date)](https://img.shields.io/github/v/release/algbio/ggcat)](https://github.com/algbio/ggcat/releases/) +[![GitHub Downloads](https://img.shields.io/github/downloads/algbio/ggcat/total.svg?style=social&logo=github&label=Download)](https://github.com/algbio/ggcat/releases) + # GGCAT - compacted and colored de Bruijn graph construction and querying GGCAT is a tool for building compacted (and optionally colored) de Bruijn graphs from raw sequencing data or for merging multiple existing cDBG in a single graph. It also supports sequence queryies to either a colored or non-colored graph (i.e. number/percentage of present kmers). +## Install + +GGCAT can be downloaded from https://github.com/algbio/ggcat/releases or installed via conda: + +``` +conda install -c conda-forge -c bioconda ggcat +``` + ## Tool usage ### Build a new graph @@ -62,6 +75,7 @@ FLAGS: -f, --forward-only Treats reverse complementary kmers as different -e, --generate-maximal-unitigs-links Generate maximal unitigs connections references, in BCALM2 format L:<+/->::<+/-> + -h, --gfa Output the graph in GFA format -g, --greedy-matchtigs Generate greedy matchtigs instead of maximal unitigs -h, --help Prints help information --keep-temp-files Keep intermediate temporary files for debugging purposes @@ -140,7 +154,7 @@ FLAGS: OPTIONS: -b, --buckets-count-log The log2 of the number of buckets - --colored-query-output-format + --colored-query-output-format -w, --hash-type Hash type used to identify kmers [default: Auto] @@ -168,9 +182,8 @@ ARGS: The input query as a .fasta file ``` -## Installation +## Building from source -At the moment building from source is the only option to install the tool. To build the tool the Rust stable (>= 1.75) toolchain is required, and can be downloaded with the following commands: ### Linux/Mac @@ -186,8 +199,6 @@ rustup toolchain install stable Follow the instructions at the site: https://rustup.rs/ -The building process was not tested on windows, but it should work with minor tweaks. - ### Additional opt-in features Additional features can be enabled by specifying them in the command line while building/installing GGCAT (ex. --features "feature1,feature2"): @@ -208,9 +219,9 @@ the binary is automatically copied to `$HOME/.cargo/bin` To launch the tool directly from the command line, the above directory should be added to the `$PATH` variable. -## Experimental API +## API usage -GGCAT has an experimental API for Rust and C++. +GGCAT has an API for both Rust and C++. ### Rust