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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


  • 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.