Difference between revisions of "FALCON"

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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.
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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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==System Variables==
 
==System Variables==
* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
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=Errors and Pitfalls=
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* 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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WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
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* [https://github.com/pb-sliang/TAP TAP] is a part of FALCON module.
  
 
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Revision as of 21:20, 6 December 2019

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.


Required Modules

Serial/Parallel

  • falcon

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.