From 24c70f23d1dda3de3c1cb6490499757f8e2b37f6 Mon Sep 17 00:00:00 2001 From: Sara Sjunnebo Date: Wed, 19 Sep 2018 15:40:28 +0100 Subject: [PATCH] fix readme and add to codecov --- .travis.yml | 10 +++++-- README.md | 82 +++++++++++++++++++++++++++++++++++++++++++++++++---- 2 files changed, 84 insertions(+), 8 deletions(-) diff --git a/.travis.yml b/.travis.yml index fde9749..79bc098 100644 --- a/.travis.yml +++ b/.travis.yml @@ -5,9 +5,13 @@ addons: - zlib1g-dev - libncurses5-dev python: - - "3.4" + - 3.4 sudo: false install: - - "source ./install_dependencies.sh" + - source ./install_dependencies.sh +before_script: + - pip install codecov script: - - "python setup.py test" + - coverage run setup.py test +after_success: + - codecov diff --git a/README.md b/README.md index bf45bda..347b3e3 100644 --- a/README.md +++ b/README.md @@ -1,10 +1,82 @@ -Circlator -========= - +# Circlator A tool to circularize genome assemblies. +[![Build Status](https://travis-ci.org/sanger-pathogens/circlator.svg?branch=master)](https://travis-ci.org/sanger-pathogens/circlator) +[![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-brightgreen.svg)](https://github.com/sanger-pathogens/circlator/blob/master/LICENSE) +[![status](https://img.shields.io/badge/GenomeBiology-10.1186-brightgreen.svg)](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0849-0) +[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](http://bioconda.github.io/recipes/circlator/README.html) +[![Container ready](https://img.shields.io/badge/container-ready-brightgreen.svg)](https://quay.io/repository/biocontainers/circlator) +[![Docker Build Status](https://img.shields.io/docker/build/sangerpathogens/circlator.svg)](https://hub.docker.com/r/sangerpathogens/circlator) +[![Docker Pulls](https://img.shields.io/docker/pulls/sangerpathogens/circlator.svg)](https://hub.docker.com/r/sangerpathogens/circlator) +[![codecov](https://codecov.io/gh/sanger-pathogens/circlator/branch/master/graph/badge.svg)](https://codecov.io/gh/sanger-pathogens/circlator) + +## Contents + * [Introduction](#introduction) + * [Installation](#installation) + * [Usage](#usage) + * [License](#license) + * [Feedback/Issues](#feedbackissues) + * [Citation](#citation) + * [Further Information](#further-information) + +## Introduction +Circlator will attempt to identify each circular sequence and output a linearised version of it. It does this by assembling all reads that map to contig ends and comparing the resulting contigs with the input assembly. + +## Installation For how to install Circlator, please see the [Circlator website](http://sanger-pathogens.github.io/circlator/). -For how to use Circlator, please see the [Circlator wiki page](https://github.com/sanger-pathogens/circlator/wiki). +## Usage +``` +Usage: circlator [options] + +To get minimal usage for a command use: +circlator command + +To get full help for a command use one of: +circlator command -h +circlator command --help + + +Available commands: + +all Run mapreads, bam2reads, assemble, merge, clean, fixstart +mapreads Map reads to assembly +bam2reads Make reads from mapping to be reassembled +assemble Run assembly using reads from bam2reads +merge Merge original assembly and new assembly made by assemble +clean Remove small and completely contained contigs from assembly +fixstart Change start position of circular sequences +minimus2 Run the minimus2 based circularisation pipeline +get_dnaa Download file of dnaA (or other of user's choice) genes +progcheck Checks dependencies are installed +test Run Circlator on a small test set +version Print version and exit +``` +For more information on how to use Circlator, please see the [Circlator wiki page](https://github.com/sanger-pathogens/circlator/wiki). + +## License +Circlator is free software, licensed under [GPLv3](https://github.com/sanger-pathogens/circlator/blob/master/LICENSE). + +## Feedback/Issues +Please report any issues to the [issues page](https://github.com/sanger-pathogens/circlator/issues) or email circlator-help@sanger.ac.uk. + +## Citation +If you use this software please cite: + +__Circlator: automated circularization of genome assemblies using long sequencing reads__ +Hunt et al, Genome Biology 2015 Dec 29;16(1):294. doi: [10.1186/s13059-015-0849-0](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0849-0) + +__[BWA](http://arxiv.org/abs/1303.3997):__ Li, H et al. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997. + +__[MUMmer](http://genomebiology.com/content/5/2/R12):__ Kurtz, S. et al. Versatile and open software for comparing large genomes. Genome Biol. 5, R12 (2004). + +__[Prodigal](http://www.biomedcentral.com/1471-2105/11/119):__ Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010). + +__[SAMtools](http://bioinformatics.oxfordjournals.org/content/25/16/2078.abstract):__ Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–9 (2009). + +__[SPAdes](http://online.liebertpub.com/doi/abs/10.1089/cmb.2012.0021)__: Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–77 (2012) -Build status: [![Build Status](https://travis-ci.org/sanger-pathogens/circlator.svg?branch=master)](https://travis-ci.org/sanger-pathogens/circlator) +## Further Information +For more information on this software see: +* the [Circlator website](http://sanger-pathogens.github.io/circlator/) +* the [Circlator wiki page](https://github.com/sanger-pathogens/circlator/wiki) \ No newline at end of file