https://github.com/gregor-mendel-institute/bookend

End-guided RNA assembler
https://github.com/gregor-mendel-institute/bookend

Last synced: about 1 month ago
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End-guided RNA assembler

• Host: GitHub
• URL: https://github.com/gregor-mendel-institute/bookend
• Owner: Gregor-Mendel-Institute
• License: mit
• Created: 2020-01-29T16:31:44.000Z (almost 5 years ago)
• Default Branch: master
• Last Pushed: 2023-10-09T12:40:38.000Z (about 1 year ago)
• Last Synced: 2024-09-30T06:06:25.782Z (about 1 month ago)
• Language: Python
• Size: 113 MB
• Stars: 15
• Watchers: 7
• Forks: 1
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# /| bookend |\\  

### End-guided transcriptome assembly.  

Bookend is a comprehensive framework for end-guided assembly of short-read, long-read, and end-capture RNA-seq data.

Please see the [User Guide](Bookend_User_Guide.pdf) for a full description of the subcommands and arguments.

The lastest developments can be found in the [Bookend GitHub repository](https://github.com/Gregor-Mendel-Institute/bookend).

Take a look at the [Bookend publication](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02700-3) for more details about its usage and applications.

## Installation  

Bookend can be installed through the Python Package Index (PyPI) on UNIX systems with Python 3.6+ using the command:

```

pip install bookend-rna --upgrade

```

If installing from the GitHub source code, perform the following steps:

```

git clone https://github.com/Gregor-Mendel-Institute/bookend

cd bookend

python3 setup.py install

```

Once installed, all utilities can be accessed on the command as bookend subcommands:  

  

    usage: bookend [subcommand] [options] [input file(s)]

    Subcommands (use -h/--help for more info):

    

        label    (Label 5' and 3' ends in a FASTQ file)

        elr      (Convert a BAM/SAM file to the end-labeled read format)

        assemble (Assemble transcripts from aligned end-labeled reads)

        condense (Partial assembly that leaves keeps all fragments; use for meta-assembly)

        classify (Compare an assembly to the transcripts of a reference annotation)

        merge    (Combine GTF files into a unified annotation)

        bedgraph (Write a coverage Bedgraph file of end-labeled reads)

        fasta    (Write a transcript FASTA file from an annotation and genome)

    

        --end-labeled read (ELR) operations--

        elr-sort

        elr-subset

        elr-combine

        

        --file conversion--

        gtf-to-bed

        gtf-ends

        bed-to-elr

        elr-to-bed

        sam-to-sj

        sj-to-bed

        sj-merge