12/7/2020 Contig Assembly Software Free Mac
Contig Assembly and Sequence Alignment. These software packages can be used to view, edit, assemble, align, BLAST and even design primers. Sequencher (Windows/OSX) v4.2 available on Mac workstations in our facility; Free and Open Source Software: Free, customizable and often times you can examine the source code. These can also be difficult.
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What Is A ContigOverview
Pilon is a software tool which can be used to:
Pilon requires as input a FASTA file of the genome along with one or more BAM files of reads aligned to the input FASTA file. Pilon uses read alignment analysis to identify inconsistencies between the input genome and the evidence in the reads. It then attempts to make improvements to the input genome, including:
Pilon then outputs a FASTA file containing an improved representation of the genome from the read data and an optional VCF file detailing variation seen between the read data and the input genome.
Contig Assembly Online
To aid manual inspection and improvement by an analyst, Pilon can optionally produce tracks that can be displayed in genome viewers such as IGV and GenomeView, and it reports other events (such as possible large collapsed repeat regions) in its standard output.
Documentation
Pilon's documentation:
License & Distribution
Binary and source releases can be found at https://github.com/broadinstitute/pilon/releases
Pilon is free software: you can redistribute it and/or modify itunder the terms of the GNU General Public LIcense version 2as published by the Free Software Foundation.
Pilon is distributed in the hope that it will be useful,but WITHOUT ANY WARRANTY; without even the implied warranty ofMERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See theGNU General Public License for more details.
Pilon source and documentation are Copyright 2012-2016 Broad Institute.
Mailing List
For announcements, questions, discussion, problem reports, etc., subscribe to the group [email protected]. If you don't have a google account, you can subscribe by sending mail to [email protected].
Download ContigCitation
If you use Pilon for published work, please cite the Pilon paper in PloS ONE:
Contig Assembly Software Free Mac Download
Citation:Bruce J. Walker, Thomas Abeel, Terrance Shea, Margaret Priest, Amr Abouelliel, Sharadha Sakthikumar, Christina A. Cuomo, Qiandong Zeng, Jennifer Wortman, Sarah K. Young, Ashlee M. Earl (2014) Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement. PLoS ONE 9(11): e112963. doi:10.1371/journal.pone.0112963
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