DNA BASER - affordable contig assembly v.2.3.2.001 Easy to use aligner software for DNA sequence contig assembly, contig editing, and mutation detection for Windows. It is a molecular biology software that can view and assemble sequences in contigs.Features: end clip, export, assemblies, detection. Dna Sequence Mac Software. DNA Baser Assembler is easy to use software for simple and batch DNA sequence assembly, DNA sequence analysis, contig editing, metadata integration and mutation detection. And is based on the same user-friendly and integrated software environment as CLC Free Workbench. Some analyses are: - Assembly of DNA.
Overview
Pilon is a software tool which can be used to:
- Automatically improve draft assemblies
- Find variation among strains, including large event detection
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:
- Single base differences
- Small indels
- Larger indel or block substitution events
- Gap filling
- Identification of local misassemblies, including optional opening of new gaps
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.
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
Contig Assembly Software Free Mac Downloads
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.
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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.
How To Use Contig
Mailing List
For announcements, questions, discussion, problem reports, etc., subscribe to the group pilon-users@broadinstitute.org. If you don't have a google account, you can subscribe by sending mail to pilon-users+subscribe@broadinstitute.org.
Citation
If you use Pilon for published work, please cite the Pilon paper in PloS ONE:
Contig Assembly Software
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