bookend-rna 0.1.3

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.

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

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)
assemble (Assemble transcripts from aligned end-labeled reads)
merge    (Merge assembled GTFs with a reference annotation)

--end-labeled read (ELR) operations--
make-elr
sort-elr
combine-elr

--file conversion--
bed-to-elr
elr-to-bed
gtf-to-bed
sam-to-sj
sj-to-bed
sj-merge

--setup/indexing--
index-fasta
softbridge-fasta