A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data

By D. Coil, Guillaume Jospin, Aaron E. Darling. Bioinform., 2014

1,070 citations recorded by the source corpus.

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.

Subfields: Ecology, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/cf1d67257681119e45c1e7e5fa7ce0f9a4dfc137

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Citations in the corpus

Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software (2017, background): “L1 Norm MetaPhyler (28) FOCUS v5 (45) TIPP (66)”
Disease-induced assemblage of a plant-beneficial bacterial consortium (2018, methodology): “paired-end reads were cleaned, trimmed and assembled using the A5-MiSeq pipeline [35] and the assembled draft”