ToFU2

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Description

tofu2 website  

This is the developmenal (ToFU2) branch of the PacBio IsoSeq analysis software. The isoform sequencing (Iso-Seq) application generates full-length cDNA sequences — from the 5’ end of transcripts to the poly-A tail — eliminating the need for transcriptome reconstruction using isoform-inference algorithms. The Iso-Seq method generates accurate information about alternatively spliced exons and transcriptional start sites. It also delivers information about poly-adenylation sites for transcripts up to 10 kb in length across the full complement of isoforms within targeted genes or the entire transcriptome.

Required Modules

System Variables

  • HPC_TOFU2_DIR - installation directory

Additional Information

To launch the singularity container ToFU2 is installed in use the 'launch_tofu2' command in a dev session shell or in a job script. E.g.

$ ml tofu2
$ launch_tofu2 run_IceInit2.py

All executables from the ToFU2 install are also directly accessible after the tofu2 module is loaded. E.g.

$ module load tofu2
$ daligner
Usage: daligner [-vbAI] [-k<int(14)>] [-w<int(6)>] [-h<int(35)>] [-t<int>] [-M<int>]
                        [-e<double(.70)] [-l<int(1000)>] [-s<int(100)>] [-H<int>] [-T<int(4)>]
                        [-m<track>]+ <subject:db|dam> <target:db|dam> ...