Stringtie¶

Description¶

StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It is primarily a genome-guided transcriptome assembler, although it can borrow algorithmic techniques from de novo genome assembly to help with transcript assembly. Its input can include not only the spliced read alignments used by reference-based assemblers, but also longer contigs that were assembled de novo from unambiguous, non-branching parts of a transcript.

Environment Modules¶

Run module spider stringtie to find out what environment modules are available for this application.

Environment Variables¶

HPC_STRINGTIE_DIR - installation directory
HPC_STRINGTIE_BIN - executable directory

Categories¶

biology, ngs, sequencing, alignment