Scallop Module Documentation

Scallop is a high-performance tool designed for the accurate and efficient quantification of transcriptome assembly. It’s capable of handling large-scale transcriptomic data while providing precise estimates of transcript abundances. Scallop’s algorithmic approach allows it to efficiently reconstruct transcript structures and quantify their expression levels, making it a valuable resource for studying gene expression and transcriptome analysis.

Shao M, Kingsford C. Accurate assembly of transcripts through phase-preserving graph decomposition. Nat Biotechnol. 2017 Dec;35(12):1167-1169. doi: 10.1038/nbt.4020. Epub 2017 Nov 13. PMID: 29131147; PMCID: PMC5722698.

ensembl.tools.anno.transcriptomic_annotation.scallop.run_scallop(output_dir: Path, scallop_bin: Path = PosixPath('scallop'), prlimit_bin: Path = PosixPath('prlimit'), stringtie_bin: Path = PosixPath('stringtie'), memory_limit: int = 42949672960) → None

Run Scallop assembler on short read data after STAR alignment.

param output_dir:

Working directory path.

type output_dir:

Path

param scallop_bin:

Software path.

type scallop_bin:

Path, default scallop

param prlimit_bin:

Software path.

type prlimit_bin:

Path, default prlimit

param stringtie_bin:

Software path.

type stringtie_bin:

Path, default stringtie

param memory_limit:

Memory limit Scallop command Defaults to 40*1024**3.

type memory_limit:

int

return:

None

rtype:

None