Stringtie Module Documentation

StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT & Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads Nature Biotechnology 2015, doi:10.1038/nbt.3122

ensembl.tools.anno.transcriptomic_annotation.stringtie.run_stringtie(output_dir: Path, stringtie_bin: Path = PosixPath('stringtie'), num_threads: int = 1) → None

StringTie assembler of short read data.

param output_dir:

Working directory path.

type output_dir:

Path

param stringtie_bin:

Software path.

type stringtie_bin:

Path, default stringtie

param num_threads:

Number of available threads.

type num_threads:

int, default 1

return:

None

rtype:

None