Metadata-Version: 2.1
Name: capture-assembler
Version: 0.1.0
Summary: The Capture seq assembler
Home-page: https://github.com/SGBC/capture
Author: Hadrien Gourlé, Renaud Van Damme
Author-email: hadrien.gourle@slu.se
License: MIT
Download-URL: https://github.com/SGBC/capture/tarball/0.1.0
Description: # The Capture-Seq assembler
        
        [![Build Status](https://travis-ci.org/SGBC/capture.svg?branch=master)](https://travis-ci.org/SGBC/capture)
        [![made-with-python](https://img.shields.io/badge/made%20with-python3-blue.svg)](https://www.python.org/)
        [![LICENSE](https://img.shields.io/badge/license-MIT-lightgrey.svg)](https://github.com/SGBC/capture)
        
        `capture` is an assembler developed to recover complete genome from ultra-high coverage samples
        
        The repository is a work in progress and the assembler is not functional yet.
        Thanks for your interest and come back soon!
        
        ## Installation
        
        `capture` requires the following to be installed:
        
        * python >= 3.6
        * SPAdes
        
        *TODO*
        
        ## Quickstart
        
        ```bash
        # paired-end reads, Illumina MiSeq
        capture assemble -f reads_R1.fastq.gz -r reads_R2.fastq.gz \
        --genome_size 35000 --mean 300 -o output_dir
        # compressed paired-end reads, Illumina HiSeq
        capture assemble -f reads_R1.fastq.gz -r reads_R2.fastq.gz \
        --genome_size 35000 --mean 125 -o output_dir
        # single end reads, Ion Torrent
        capture assemble -u reads.fastq.gz \
        --genome_size 35000 --mean 240 -o output_dir
        # reads in bam format
        capture assemble --bam reads.bam \
        --genome_size 35000 --mean 240 -o output_dir
        # full list of subcommands and options
        capture -h
        # full list of options for a subcommand
        capture assemble -h
        ```
        
        ## License
        
        Code is under the [MIT](LICENSE) license
        
        ## Contributing
        
        We welcome contributions from the community! See our [Contributing](CONTRIBUTING.md) guide.
        
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