KO
|
EN
gitlite — search
Search
#python
#java
#javascript
#php
#dotfiles
#c-plus-plus
#html
#django
#nodejs
#lua
#go
#symfony
clockwork
★ 35
Open GitHub ↗
CRyPTIC data processing pipelines
Download README (.md)
Explore Similar Repositories
lsi_decode_loginfo
:
Decode LSI LogInfo codes to make troubleshooting slightly less cryptic
crypticos
:
Obscure 256 Byte OS
sudocle
:
A modern web app for Sudoku inspired by Cracking the Cryptic
CryptoBench
:
Scripts for the creation of CryptoBench, a new dataset of cryptic binding sites
cryptic-scenario-modeling-hub
:
Pandemic cryptic phase modeling hub
// repository documentation
Was this content helpful?
★ 0
(0 ratings)
Select Rating:
★
★
★
★
★
Submit Feedback
Recent Feedback
×
Download README
Do you want to download the
README.md
file for
clockwork
?
Download (.md)
# Clockwork ## Pipelines for processing bacterial sequence data (Illumina only) and variant calling Note: these pipelines were developed for the [CRyPTIC](http://www.crypticproject.org/) project which studies _M. tuberculosis_, but in principle can be used on any bacteria. Clockwork takes fastq input and outputs standard VCF files as output Please see the [clockwork wiki page](https://github.com/iqbal-lab-org/clockwork/wiki) for documentation. ## Citation If you use Clockwork for variant calling please cite the following paper, where it was introduced and benchmarked: "Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes". Hunt et al. Genome Biol. 2022 Jul 5;23(1):147. [doi: 10.1186/s13059-022-02714-x.](https://doi.org/10.1186/s13059-022-02714-x) Whilst Minos is the novel part of the Clockwork variant calling pipeline, it uses several other tools. Please also cite: * Minimap2 https://doi.org/10.1093/bioinformatics/bty191 * SAMtools https://doi.org/10.1093/gigascience/giab008 * Cortex https://doi.org/10.1038/ng.1028 * Trimmomatic: https://doi.org/10.1093/bioinformatics/btu170
