pbtranscript-tofu

Description

pbtranscript-tofu website

Scripts for processing PacBio transcriptome (Iso-Seq) data. The scripts in this repository are now compatible with SMRTAnalysis 2.3. It is a "beta" version of the RS_IsoSeq protocol that is supported in 2.3, meaning that it extends the existing RS_IsoSeq code base, and is an unofficial, developemental version of RS_IsoSeq. This beta version is only accessible via command line. The command line name of the official RS_IsoSeq is pbtranscript, to differentiate from the official version, in the tutorials we will refer to the beta version provided on this site as pbtranscript-tofu. Functionality provided in pbtranscript-tofu is highly developmental and may not make it into the next version of official RS_IsoSeq. Latest version of pbtranscript-tofu contains the following extensions: * tofu_wrap.py is a wrapper around pbtranscript.py that automatically divides input into different size bins, runs clustering on the individual bins and combines them later, reducing unnecessary memory usage & runtime. * Support for "--fasta_fofn" input; also using multi-core for generating .bax.h5.fasta files for speedup. * Support for collapsing redundant transcripts based on alignment SAM file. * "fusion_finder.py" is a script for finding fusion transcripts from an aligned sorted SAM file. * Minor changes to better support SMRTAnalysis 2.3 framework.

Environment Modules

Run module spider pbtranscript-tofu to find out what environment modules are available for this application.

Environment Variables

• HPC_PBTRANCRIPT_DIR - installation directory

Categories

biology, ngs