Difference between revisions of "FALCON"

From UFRC
Jump to navigation Jump to search
 
(5 intermediate revisions by 3 users not shown)
Line 1: Line 1:
[[Category:Software]][[Category:Bioinformatics]][[Category:NGS]]
+
[[Category:Software]][[Category:Biology]][[Category:NGS]][[Category:Sequencing]]
 
{|<!--CONFIGURATION: REQUIRED-->
 
{|<!--CONFIGURATION: REQUIRED-->
 
|{{#vardefine:app|falcon}}
 
|{{#vardefine:app|falcon}}
Line 22: Line 22:
 
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.
  
  
 
<!--Modules-->
 
<!--Modules-->
==Required Modules==
+
==Environment Modules==
===Serial/Parallel===
+
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
* {{#var:app}}
 
<!--
 
===Parallel (MPI)===
 
* intel
 
* openmpi
 
* {{#var:app}}
 
-->
 
 
==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
+
* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 
<!--Configuration-->
 
<!--Configuration-->
 
{{#if: {{#var: conf}}|==Configuration==
 
{{#if: {{#var: conf}}|==Configuration==
Line 45: Line 38:
 
=Errors and Pitfalls=
 
=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.
 
* 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.
 +
 +
 +
* [https://github.com/pb-sliang/TAP TAP] is a part of FALCON module.
  
 
|}}
 
|}}

Latest revision as of 15:19, 15 August 2022

Description

falcon website  

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.