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Falcon

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.

DOCUMENTATION

Please check doc/falcon_manual.md

ABOUT THE LICENSE

Standard PacBio Open Source License that is associated with this package:

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# Copyright (c) 2011-2014, Pacific Biosciences of California, Inc.
#
# All rights reserved.
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# Redistribution and use in source and binary forms, with or without
# modification, are permitted (subject to the limitations in the
# disclaimer below) provided that the following conditions are met:
#
#  * Redistributions of source code must retain the above copyright
#  notice, this list of conditions and the following disclaimer.
#
#  * Redistributions in binary form must reproduce the above
#  copyright notice, this list of conditions and the following
#  disclaimer in the documentation and/or other materials provided
#  with the distribution.
#
#  * Neither the name of Pacific Biosciences nor the names of its
#  contributors may be used to endorse or promote products derived
#  from this software without specific prior written permission.
#
# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
# GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
# BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
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# DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
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# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
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# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
# OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
# SUCH DAMAGE.
#################################################################################$$

--Jason Chin, Dec 1, 2014

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FALCON: experimental PacBio diploid assembler

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  • Python 86.8%
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