Difference between revisions of "FALCON"
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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. | 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. | ||
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{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
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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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Revision as of 02:24, 14 December 2016
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.
Required Modules
Serial/Parallel
- falcon
System Variables
- HPC_{{#uppercase: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.