From d6974d2efff90e90f6e46726d006ddfb6427b3b2 Mon Sep 17 00:00:00 2001 From: gbouras13 Date: Tue, 21 Nov 2023 12:06:42 +1030 Subject: [PATCH] update docs and readme [skip ci] --- HISTORY.md | 6 ++++++ README.md | 40 ++++++++++++++++++++++++++-------------- 2 files changed, 32 insertions(+), 14 deletions(-) diff --git a/HISTORY.md b/HISTORY.md index 2e16ac1..f73bf92 100644 --- a/HISTORY.md +++ b/HISTORY.md @@ -1,5 +1,11 @@ # History +1.5.0 (2023-11-21) +------------------ + +* **If you upgrade to v1.5.0, you will need to update the database using `plassembler download`** +* Plassembler v1.5.0 incorporates a new database thanks to the recent PLSDB release [2023_11_03_v2](https://ccb-microbe.cs.uni-saarland.de/plsdb/). Thanks @[biobrad](https://github.com/biobrad) for the heads up. + 1.4.1 (2023-10-30) ------------------ diff --git a/README.md b/README.md index c74f275..bd44979 100644 --- a/README.md +++ b/README.md @@ -24,6 +24,22 @@ Additionally, I would recommend reading the following guides to bacterial genome * [Perfect Bacterial Assembly Tutorial](https://github.com/rrwick/Perfect-bacterial-genome-tutorial) * [Perfect bacterial assembly Paper](https://doi.org/10.1371/journal.pcbi.1010905) +## Quick Start + +The easiest way to install `plassembler` is via conda: + +`conda install -c bioconda plassembler` + +Followed by database download and installation: + +`plassembler download -d ` + +And finally run `plassembler`: + +`plassembler run -d -l -o -1 < short read R1 fastq> -2 < short read R2 fastq> -c ` + +Please read the [Installation](#installation) section for more details, especially if you are an inexperienced command line user. + ## Manuscript `plassembler` has been recently published in *Bioinformatics*: @@ -32,13 +48,19 @@ George Bouras, Anna E. Sheppard, Vijini Mallawaarachchi, Sarah Vreugde, Plassemb If you use `plassembler`, please see the full [Citations](#citations) section for a list of all programs `plassembler` uses under the hood, in order to fully recognise the creators of these tools for their work. +## Documentation + +The full documentation for Plassembler can be found [here](https://plassembler.readthedocs.io/en/latest). + ## Table of Contents - [plassembler](#plassembler) - [Automated Bacterial Plasmid Assembly Program](#automated-bacterial-plasmid-assembly-program) + - [Quick Start](#quick-start) - [Manuscript](#manuscript) + - [Documentation](#documentation) - [Table of Contents](#table-of-contents) - - [Quick Start](#quick-start) + - [`plassembler` v1.5.0 Update New Database (21 November 2023)](#plassembler-v150-update-new-database-21-november-2023) - [`plassembler` v1.3.0 Updates (24 October 2023)](#plassembler-v130-updates-24-october-2023) - [Why Does Plassembler Exist?](#why-does-plassembler-exist) - [Why Not Just Use Unicycler?](#why-not-just-use-unicycler) @@ -58,21 +80,11 @@ If you use `plassembler`, please see the full [Citations](#citations) section fo - [Bugs and Suggestions](#bugs-and-suggestions) - [Citations](#citations) -## Quick Start - -The easiest way to install `plassembler` is via conda: - -`conda install -c bioconda plassembler` - -Followed by database download and installation: - -`plassembler download -d ` - -And finally run `plassembler`: +## `plassembler` v1.5.0 Update New Database (21 November 2023) -`plassembler run -d -l -o -1 < short read R1 fastq> -2 < short read R2 fastq> -c ` +* **If you upgrade to v1.5.0, you will need to update the database using `plassembler download`** +* Plassembler v1.5.0 incorporates a new expanded database thanks to the recent PLSDB release [2023_11_03_v2](https://ccb-microbe.cs.uni-saarland.de/plsdb/). Thanks @[biobrad](https://github.com/biobrad) for the heads up. -Please read the [Installation](#installation) section for more details, especially if you are an inexperienced command line user. ## `plassembler` v1.3.0 Updates (24 October 2023)