stringtie
assemble short RNAseq reads to transcripts
Command lineScience
Not tested on a device yet. What that means
Commands in the package
stringtieprepDE.py
About stringtie
From Debian's package description
The abundance of transcripts in a human tissue sample can be determined by RNA sequencing. The exact sequence sampled may be random, depending on the technology used. And it may be short, i.e. shorter than the transcript. At some point, many shorter reads need to be assembled to the model the complete transcripts.
StringTie knows how to assemble of RNA-Seq into potential transcripts without the need of a reference genome and provides a quantification also of the splice variants.
From Debian's description of the stringtie package, under that package's license.
Dependencies
Depends on
libc6libhts3t64libstdc++6python3
Recommends
stringtie-examples
On x86-64 it also needs libgcc-s1.
Related apps
- bowtie2ultrafast memory-efficient short read alignerCommand line
- bowtieUltrafast memory-efficient short read alignerCommand line
- hisat2graph-based alignment of short nucleotide reads to many genomesCommand line
- macsModel-based Analysis of ChIP-Seq on short reads sequencersCommand line
- bitseqBayesian Inference of Transcripts from Sequencing DataCommand line
- salmonwicked-fast transcript quantification from RNA-seq dataCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the stringtie package, under that package's license.
- Description: Debian's description of the stringtie package, under that package's license.
- Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
- Popularity: Debian Popularity Contest counts.
More in About the catalog.