Scallop#
Scallop is a high-performance tool designed for the accurate and efficient quantification
API#
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.
References
[10]
- ensembl.tools.anno.transcriptomic_annotation.scallop.run_scallop(output_dir, scallop_bin=PosixPath('scallop'), prlimit_bin=PosixPath('prlimit'), stringtie_bin=PosixPath('stringtie'), memory_limit=42949672960)[source]#
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