Metadata-Version: 2.1
Name: bookend-rna
Version: 1.0.1
Summary: End-guided transcript assembler for short and long RNA-seq reads.
Home-page: https://github.com/Gregor-Mendel-Institute/bookend
Author: Michael A. Schon
Author-email: michael.schon@gmi.oeaw.ac.at
License: UNKNOWN
Description: # /| 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).
        
        ## 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
        ```
        
        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)
                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
        
Keywords: transcriptome assembler bioinformatics rna sequencing
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
