View source for ToFU2

[[Category:Software]][[Category:Biology]]
{|<!--CONFIGURATION: REQUIRED-->
|{{#vardefine:app|tofu2}}
|{{#vardefine:url|https://github.com/PacificBiosciences/IsoSeq_SA3nUP/wiki}}
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|{{#vardefine:conf|}}           <!--CONFIGURATION-->
|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
|{{#vardefine:job|}}            <!--JOB SCRIPTS-->
|{{#vardefine:policy|}}         <!--POLICY-->
|{{#vardefine:testing|}}       <!--PROFILING-->
|{{#vardefine:faq|}}             <!--FAQ-->
|{{#vardefine:citation|}}       <!--CITATION-->
|{{#vardefine:installation|}} <!--INSTALLATION-->
|}
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<!--Description-->
{{#if: {{#var: url}}|
{{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-->
==Required Modules==
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===Serial===
* {{#var:app}}
===Parallel (OpenMP)===
* intel
* {{#var:app}}
===Parallel (MPI)===
* intel
* openmpi
* {{#var:app}}
-->
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
<!--Configuration-->
{{#if: {{#var: conf}}|==Configuration==
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
|}}
<!--Run-->
{{#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-->
{{#if: {{#var: job}}|==Job Script Examples==
See the [[{{PAGENAME}}_Job_Scripts]] page for {{#var: app}} Job script examples.
|}}
<!--Policy-->
{{#if: {{#var: policy}}|==Usage Policy==

WRITE USAGE POLICY HERE (Licensing, usage, access).

|}}
<!--Performance-->
{{#if: {{#var: testing}}|==Performance==

WRITE_PERFORMANCE_TESTING_RESULTS_HERE

|}}
<!--Faq-->
{{#if: {{#var: faq}}|==FAQ==
*'''Q:''' **'''A:'''|}}
<!--Citation-->
{{#if: {{#var: citation}}|==Citation==
If you publish research that uses {{#var:app}} you have to cite it as follows:

WRITE_CITATION_HERE

|}}
<!--Installation-->
{{#if: {{#var: installation}}|==Installation==
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
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