Difference between revisions of "FALCON"
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Sequencing]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|falcon}} | |{{#vardefine:app|falcon}} | ||
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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:pbs|}} <!--PBS SCRIPTS--> | |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
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The Falcon tool kit is a set of simple code collection which I use for studying efficient assembly algorithm for haploid and diploid genomes. It has some back-end code implemented in C for speed and some simple front-end written in Python for convenience. | The Falcon tool kit is a set of simple code collection which I use for studying efficient assembly algorithm for haploid and diploid genomes. It has some back-end code implemented in C for speed and some simple front-end written in Python for convenience. | ||
| − | We use FALCON-integrate in conjunction with SLURM to run FALCON on HiPerGator. See the [[FALCON_fc_run_cfg|sample SLURM fc_run.cfg]] for an example. | + | We use FALCON-integrate in conjunction with SLURM to run FALCON on HiPerGator. See the [[FALCON_fc_run_cfg|sample SLURM fc_run.cfg]] for an example. For a larger run consider modifying DAligner options to set a memory limit on kmer search with -M. See [[FALCON_fc_large_run_cfg|sample SLURM fc_large_run.cfg]] for an example. |
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<!--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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| − | < | ||
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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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<!--Run--> | <!--Run--> | ||
{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
| + | =Errors and Pitfalls= | ||
| + | * Make sure that the fasta headers are in a format acceptable to FALCON. If you encounterd a Fasta2DB error '<code>Line 1: Pacbio header line format error</code>' see [https://github.com/PacificBiosciences/FALCON/issues/251 FALCON issue #251] for an explanation. | ||
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| − | + | * [https://github.com/pb-sliang/TAP TAP] is a part of FALCON module. | |
|}} | |}} | ||
Latest revision as of 15:19, 15 August 2022
Description
Falcon: a set of tools for fast aligning long reads for consensus and assembly
The Falcon tool kit is a set of simple code collection which I use for studying efficient assembly algorithm for haploid and diploid genomes. It has some back-end code implemented in C for speed and some simple front-end written in Python for convenience.
We use FALCON-integrate in conjunction with SLURM to run FALCON on HiPerGator. See the sample SLURM fc_run.cfg for an example. For a larger run consider modifying DAligner options to set a memory limit on kmer search with -M. See sample SLURM fc_large_run.cfg for an example.
Environment Modules
Run module spider falcon to find out what environment modules are available for this application.
System Variables
- HPC_FALCON_DIR - installation directory
Additional Information
Errors and Pitfalls
- Make sure that the fasta headers are in a format acceptable to FALCON. If you encounterd a Fasta2DB error '
Line 1: Pacbio header line format error' see FALCON issue #251 for an explanation.
- TAP is a part of FALCON module.