/| 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
