bookend-rna 1.2.1

End-guided transcript assembler for short and long RNA-seq reads.

/| 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 for a full description of the subcommands and arguments. The lastest developments can be found in the Bookend GitHub repository.

Take a look at the Bookend publication 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