Name: Description: DNA Sequence Assembler: DNA Baser is a tool for DNA Sequence Assembler, DNA sequence analysis, contig editing, and mutation detection.It also offers a powerful chromatogram viewer/editor. Command line. DNA Sequence Assembler is now available soon also as a command line tool so you can call it from your own code/scripts. And Madan, A. (1999) CAP3: A DNA sequence assembly program. Genome Res., 9, 868-877. For a more advanced usage of CAP3, it is recommended to install the original software on.

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1. Cap3 Contig Assembly
2. Contig Sequence
3. Contig Assembly Software Free Mac Software
4. Contig Assembly Software Free Mac Download

Overview

Pilon is a software tool which can be used to:

• Automatically improve draft assemblies
• Find variation among strains, including large event detection

EnsembleAssembler optimizes contig formation by integrating results from multiple assemblers including SOAPDenovo2, ABySS, MetaVelvet, and Cap3. The software does NOT perform preprocessing. The user needs to do preprocessing with other software before attempting for assembly. If you need to work on 8086 assembler for developing or studying, 8086 ASM is for you.This is the free version, only ADD and MOV commands are. Free Publisher: Francesco Crema Downloads: 76.

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:

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Cap3 Contig Assembly

• 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:

Contig Sequence

License & Distribution

Binary and source releases can be found at https://github.com/broadinstitute/pilon/releases

Contig Assembly Software Free Mac Software

Contig Assembly Software Free Mac Download

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].

Citation

If you use Pilon for published work, please cite the Pilon paper in PloS ONE:

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