A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data
Motivation: Open-source bacterial genome assembly remains inaccessible to many biologists because of its complexity. Few software solutions exist that are capable of automating all steps in the process of de novo genome assembly from Illumina data. Results: A5-miseq can produce high-quality microbia...
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| Published in | Bioinformatics (Oxford, England) Vol. 31; no. 4; pp. 587 - 589 |
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| Main Authors | , , |
| Format | Journal Article |
| Language | English |
| Published |
England
15.02.2015
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| Subjects | |
| Online Access | Get full text |
| ISSN | 1367-4803 1367-4811 1367-4811 |
| DOI | 10.1093/bioinformatics/btu661 |
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| Abstract | Motivation: Open-source bacterial genome assembly remains inaccessible to many biologists because of its complexity. Few software solutions exist that are capable of automating all steps in the process of de novo genome assembly from Illumina data.
Results: A5-miseq can produce high-quality microbial genome assemblies on a laptop computer without any parameter tuning. A5-miseq does this by automating the process of adapter trimming, quality filtering, error correction, contig and scaffold generation and detection of misassemblies. Unlike the original A5 pipeline, A5-miseq can use long reads from the Illumina MiSeq, use read pairing information during contig generation and includes several improvements to read trimming. Together, these changes result in substantially improved assemblies that recover a more complete set of reference genes than previous methods.
Availability: A5-miseq is licensed under the GPL open-source license. Source code and precompiled binaries for Mac OS X 10.6+ and Linux 2.6.15+ are available from http://sourceforge.net/projects/ngopt
Contact: aaron.darling@uts.edu.au
Supplementary information: Supplementary Data are available at Bioinformatics online. |
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| AbstractList | Open-source bacterial genome assembly remains inaccessible to many biologists because of its complexity. Few software solutions exist that are capable of automating all steps in the process of de novo genome assembly from Illumina data.MOTIVATIONOpen-source bacterial genome assembly remains inaccessible to many biologists because of its complexity. Few software solutions exist that are capable of automating all steps in the process of de novo genome assembly from Illumina data.A5-miseq can produce high-quality microbial genome assemblies on a laptop computer without any parameter tuning. A5-miseq does this by automating the process of adapter trimming, quality filtering, error correction, contig and scaffold generation and detection of misassemblies. Unlike the original A5 pipeline, A5-miseq can use long reads from the Illumina MiSeq, use read pairing information during contig generation and includes several improvements to read trimming. Together, these changes result in substantially improved assemblies that recover a more complete set of reference genes than previous methods.RESULTSA5-miseq can produce high-quality microbial genome assemblies on a laptop computer without any parameter tuning. A5-miseq does this by automating the process of adapter trimming, quality filtering, error correction, contig and scaffold generation and detection of misassemblies. Unlike the original A5 pipeline, A5-miseq can use long reads from the Illumina MiSeq, use read pairing information during contig generation and includes several improvements to read trimming. Together, these changes result in substantially improved assemblies that recover a more complete set of reference genes than previous methods.A5-miseq is licensed under the GPL open-source license. Source code and precompiled binaries for Mac OS X 10.6+ and Linux 2.6.15+ are available from http://sourceforge.net/projects/ngoptAVAILABILITYA5-miseq is licensed under the GPL open-source license. Source code and precompiled binaries for Mac OS X 10.6+ and Linux 2.6.15+ are available from http://sourceforge.net/projects/ngoptaaron.darling@uts.edu.auCONTACTaaron.darling@uts.edu.auSupplementary data are available at Bioinformatics online.SUPPLEMENTARY INFORMATIONSupplementary data are available at Bioinformatics online. Open-source bacterial genome assembly remains inaccessible to many biologists because of its complexity. Few software solutions exist that are capable of automating all steps in the process of de novo genome assembly from Illumina data. A5-miseq can produce high-quality microbial genome assemblies on a laptop computer without any parameter tuning. A5-miseq does this by automating the process of adapter trimming, quality filtering, error correction, contig and scaffold generation and detection of misassemblies. Unlike the original A5 pipeline, A5-miseq can use long reads from the Illumina MiSeq, use read pairing information during contig generation and includes several improvements to read trimming. Together, these changes result in substantially improved assemblies that recover a more complete set of reference genes than previous methods. A5-miseq is licensed under the GPL open-source license. Source code and precompiled binaries for Mac OS X 10.6+ and Linux 2.6.15+ are available from http://sourceforge.net/projects/ngopt aaron.darling@uts.edu.au Supplementary data are available at Bioinformatics online. Motivation: Open-source bacterial genome assembly remains inaccessible to many biologists because of its complexity. Few software solutions exist that are capable of automating all steps in the process of de novo genome assembly from Illumina data. Results: A5-miseq can produce high-quality microbial genome assemblies on a laptop computer without any parameter tuning. A5-miseq does this by automating the process of adapter trimming, quality filtering, error correction, contig and scaffold generation and detection of misassemblies. Unlike the original A5 pipeline, A5-miseq can use long reads from the Illumina MiSeq, use read pairing information during contig generation and includes several improvements to read trimming. Together, these changes result in substantially improved assemblies that recover a more complete set of reference genes than previous methods. Availability: A5-miseq is licensed under the GPL open-source license. Source code and precompiled binaries for Mac OS X 10.6+ and Linux 2.6.15+ are available from http://sourceforge.net/projects/ngopt Contact: aaron.darling@uts.edu.au Supplementary information: Supplementary Data are available at Bioinformatics online. |
| Author | Darling, Aaron E. Coil, David Jospin, Guillaume |
| Author_xml | – sequence: 1 givenname: David surname: Coil fullname: Coil, David – sequence: 2 givenname: Guillaume surname: Jospin fullname: Jospin, Guillaume – sequence: 3 givenname: Aaron E. surname: Darling fullname: Darling, Aaron E. |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/25338718$$D View this record in MEDLINE/PubMed |
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| Cites_doi | 10.1093/bioinformatics/btt086 10.1093/bioinformatics/bts174 10.1371/journal.pone.0042304 10.1089/cmb.2012.0021 10.1093/bioinformatics/btt273 10.1101/gr.126953.111 10.1093/nar/gks540 |
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