circlator

A tool to circularize genome assemblies

https://github.com/sanger-pathogens/circlator

Science Score: 54.0%

This score indicates how likely this project is to be science-related based on various indicators:

○
CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
○
.zenodo.json file
✓
DOI references
Found 4 DOI reference(s) in README
✓
Academic publication links
Links to: arxiv.org
✓
Committers with academic emails
8 of 19 committers (42.1%) from academic institutions
✓
Institutional organization owner
Organization sanger-pathogens has institutional domain (www.sanger.ac.uk)
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (12.6%) to scientific vocabulary

Keywords

bioinformatics bioinformatics-pipeline genomics global-health infectious-diseases next-generation-sequencing pathogen research sequencing

Keywords from Contributors

sequence-alignment comparative-genomics

Last synced: 6 months ago · JSON representation

Repository

A tool to circularize genome assemblies

Basic Info

Host: GitHub
Owner: sanger-pathogens
License: other
Language: Python
Default Branch: master
Homepage: http://sanger-pathogens.github.io/circlator/
Size: 25.7 MB

Statistics

Stars: 247
Watchers: 20
Forks: 57
Open Issues: 60
Releases: 36

Topics

bioinformatics bioinformatics-pipeline genomics global-health infectious-diseases next-generation-sequencing pathogen research sequencing

Created almost 11 years ago · Last pushed almost 2 years ago

Metadata Files

Readme Changelog License Authors

Circlator

A tool to circularize genome assemblies.

PLEASE NOTE: we currently do not have the resources to provide support for Circlator, so please do not expect a reply if you flag any issue. Apologies for the inconvenience.

Introduction
Installation
Usage
License
Feedback/Issues
Citation
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.

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.

License

Circlator is free software, licensed under GPLv3.

Feedback/Issues

Please report any issues to the issues page.

PLEASE NOTE: we currently do not have the resources to provide support for Circlator, so please do not expect a reply if you flag any issue. Apologies for the inconvenience.

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

BWA: Li, H et al. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997.

MUMmer: Kurtz, S. et al. Versatile and open software for comparing large genomes. Genome Biol. 5, R12 (2004).

Prodigal: Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010).

SAMtools: Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–9 (2009).

SPAdes: Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–77 (2012)

Further Information

For more information on this software see: * the Circlator website * the Circlator wiki page

Owner

Name: Pathogen Informatics, Wellcome Sanger Institute
Login: sanger-pathogens
Kind: organization
Location: Hinxton, Cambs., UK

Website: http://www.sanger.ac.uk/science/groups/pathogen-informatics
Repositories: 54
Profile: https://github.com/sanger-pathogens

GitHub Events

Total

Watch event: 16
Member event: 1
Issue comment event: 3
Pull request event: 2
Fork event: 1

Last Year

Watch event: 16
Member event: 1
Issue comment event: 3
Pull request event: 2
Fork event: 1

Committers

Last synced: over 2 years ago

All Time

Total Commits: 305
Total Committers: 19
Avg Commits per committer: 16.053
Development Distribution Score (DDS): 0.249

Past Year

Commits: 2
Committers: 2
Avg Commits per committer: 1.0
Development Distribution Score (DDS): 0.5

Top Committers

Name	Email	Commits
Martin Hunt	m**2@s**k	229
Martin Hunt	m**t@g**m	26
andrewjpage	a**e@g**m	9
Tim Stickland	t**4@s**k	6
Sara Sjunnebo	s**4@s**k	6
Nicola De Maio	n**o@n**k	5
martinghunt	m****t	4
martinghunt	m**t@g**m	4
Bastian Greshake	b**e@g**m	3
Gareth Peat	g**6@s**k	3
puethe	c**5@s**k	2
Nilesh Patra	n**h@d**g	1
Yuri Bendana	y**a@s**m	1
ssjunnebo	s**o@g**m	1
William Roberts	w**7@s**k	1
Bogdan	t**n@g**m	1
Martin Aslett	m**a@s**k	1
Michael R. Crusoe	c**e@d**g	1
Jason Stajich	j**d@g**m	1

Committer Domains (Top 20 + Academic)

sanger.ac.uk: 7 debian.org: 2 sangamo.com: 1 ndm.ox.ac.uk: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 80
Total pull requests: 28
Average time to close issues: 4 months
Average time to close pull requests: 24 days
Total issue authors: 65
Total pull request authors: 17
Average comments per issue: 1.54
Average comments per pull request: 0.21
Merged pull requests: 21
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 1
Pull requests: 2
Average time to close issues: N/A
Average time to close pull requests: about 2 months
Issue authors: 1
Pull request authors: 1
Average comments per issue: 0.0
Average comments per pull request: 1.0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

yjx1217 (5)
caonetto (3)
MattPinder (2)
bitcometz (2)
zhaoxvwahaha (2)
EricDeveaud (2)
tseemann (2)
mictadlo (2)
nataliering (2)
lfaller (2)
conchoecia (2)
martinghunt (1)
samfux84 (1)
isabelluo (1)
s4251484 (1)

Pull Request Authors

ssjunnebo (8)
trstickland (4)
ramongallego (2)
Adamtaranto (2)
matt-plumb (1)
puethe (1)
Lfulcrum (1)
ybendana (1)
spock (1)
pathdevg (1)
hyphaltip (1)
garethpeat (1)
andrewjpage (1)
martinghunt (1)
HieuVoDL (1)

Top Labels

Issue Labels

enhancement (3) question (2) installation (2) wontfix (2) invalid (2) bug (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- pypi 122 last-month

Total dependent packages: 0
Total dependent repositories: 6
Total versions: 33
Total maintainers: 2

pypi.org: circlator

circlator: a tool to circularise genome assemblies

Homepage: https://github.com/sanger-pathogens/circlator
Documentation: https://circlator.readthedocs.io/
License: GPLv3
Latest release: 1.5.5
published about 8 years ago

Versions: 33
Dependent Packages: 0
Dependent Repositories: 6
Downloads: 122 Last month
Docker Downloads: 0

Rankings

Docker downloads count: 1.5%

Stargazers count: 4.8%

Forks count: 5.8%

Dependent repos count: 6.0%

Average: 8.1%

Dependent packages count: 10.0%

Downloads: 20.6%

Maintainers (2)

sanger-pathogens martinghunt

Last synced: 6 months ago

Dependencies

setup.py pypi

openpyxl *
pyfastaq *
pymummer >=0.9.0
pysam *

Dockerfile docker

ubuntu 16.04 build

circlator

Science Score: 54.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

Circlator

Contents

Introduction

Installation

Usage

License

Feedback/Issues

Citation

Further Information

Owner

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

pypi.org: circlator

Rankings

Maintainers (2)

Dependencies