Difference between revisions of "ToFU2"
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Moskalenko (talk | contribs) (Created page with "Category:SoftwareCategory:Biology {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|tofu2}} |{{#vardefine:url|https://github.com/PacificBiosciences/IsoSeq_SA3nUP/wiki...") |
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| − | [[Category:Software]][[Category:Biology]] | + | [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Sequencing]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|tofu2}} | |{{#vardefine:app|tofu2}} | ||
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<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
| − | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
|{{#vardefine:job|}} <!--JOB SCRIPTS--> | |{{#vardefine:job|}} <!--JOB SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | ||
| − | + | 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. | |
<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | < | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. |
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
| − | + | To launch the singularity container ToFU2 is installed in use the 'launch_tofu2' command in a [[Development_and_Testing|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 | ||
| + | <pre> | ||
| + | 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> ... | ||
| + | </pre> | ||
|}} | |}} | ||
<!--Job Scripts--> | <!--Job Scripts--> | ||
Latest revision as of 16:38, 22 August 2022
Description
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.
Environment Modules
Run module spider tofu2 to find out what environment modules are available for this application.
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> ...