# /| 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
Raw data
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"description": "# /| bookend |\\\\ \n### End-guided transcriptome assembly. \nBookend is a comprehensive framework for end-guided assembly of short-read, long-read, and end-capture RNA-seq data.\nPlease see the [User Guide](Bookend_User_Guide.pdf) for a full description of the subcommands and arguments.\nThe lastest developments can be found in the [Bookend GitHub repository](https://github.com/Gregor-Mendel-Institute/bookend).\n\nTake 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.\n\n## Installation \nBookend can be installed through the Python Package Index (PyPI) on UNIX systems with Python 3.6+ using the command:\n```\npip install bookend-rna --upgrade\n```\n\nIf installing from the GitHub source code, perform the following steps:\n```\ngit clone https://github.com/Gregor-Mendel-Institute/bookend\ncd bookend\npython3 setup.py install\n```\n\nOnce installed, all utilities can be accessed on the command as bookend subcommands: \n \n usage: bookend [subcommand] [options] [input file(s)]\n Subcommands (use -h/--help for more info):\n \n label (Label 5' and 3' ends in a FASTQ file)\n elr (Convert a BAM/SAM file to the end-labeled read format)\n assemble (Assemble transcripts from aligned end-labeled reads)\n condense (Partial assembly that leaves keeps all fragments; use for meta-assembly)\n classify (Compare an assembly to the transcripts of a reference annotation)\n merge (Combine GTF files into a unified annotation)\n bedgraph (Write a coverage Bedgraph file of end-labeled reads)\n fasta (Write a transcript FASTA file from an annotation and genome)\n \n --end-labeled read (ELR) operations--\n elr-sort\n elr-subset\n elr-combine\n \n --file conversion--\n gtf-to-bed\n gtf-ends\n bed-to-elr\n elr-to-bed\n sam-to-sj\n sj-to-bed\n sj-merge \n\n\n",
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