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      Is Open Access

      aTRAM 2.0: An Improved, Flexible Locus Assembler for NGS Data

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          Abstract

          Massive strides have been made in technologies for collecting genome-scale data. However, tools for efficiently and flexibly assembling raw outputs into downstream analytical workflows are still nascent. aTRAM 1.0 was designed to assemble any locus from genome sequencing data but was neither optimized for efficiency nor able to serve as a single toolkit for all assembly needs. We have completely re-implemented aTRAM and redesigned its structure for faster read retrieval while adding a number of key features to improve flexibility and functionality. The software can now (1) assemble single- or paired-end data, (2) utilize both read directions in the database, (3) use an additional de novo assembly module, and (4) leverage new built-in pipelines to automate common workflows in phylogenomics. Owing to reimplementation of databasing strategies, we demonstrate that aTRAM 2.0 is much faster across all applications compared to the previous version.

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          Most cited references9

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          Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales.

          Although massively parallel sequencing has facilitated large-scale DNA sequencing, comparisons among distantly related species rely upon small portions of the genome that are easily aligned. Methods are needed to efficiently obtain comparable DNA fragments prior to massively parallel sequencing, particularly for biologists working with non-model organisms. We introduce a new class of molecular marker, anchored by ultraconserved genomic elements (UCEs), that universally enable target enrichment and sequencing of thousands of orthologous loci across species separated by hundreds of millions of years of evolution. Our analyses here focus on use of UCE markers in Amniota because UCEs and phylogenetic relationships are well-known in some amniotes. We perform an in silico experiment to demonstrate that sequence flanking 2030 UCEs contains information sufficient to enable unambiguous recovery of the established primate phylogeny. We extend this experiment by performing an in vitro enrichment of 2386 UCE-anchored loci from nine, non-model avian species. We then use alignments of 854 of these loci to unambiguously recover the established evolutionary relationships within and among three ancient bird lineages. Because many organismal lineages have UCEs, this type of genetic marker and the analytical framework we outline can be applied across the tree of life, potentially reshaping our understanding of phylogeny at many taxonomic levels.
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            Genome assembly reborn: recent computational challenges.

            Mihai Pop (2009)
            Research into genome assembly algorithms has experienced a resurgence due to new challenges created by the development of next generation sequencing technologies. Several genome assemblers have been published in recent years specifically targeted at the new sequence data; however, the ever-changing technological landscape leads to the need for continued research. In addition, the low cost of next generation sequencing data has led to an increased use of sequencing in new settings. For example, the new field of metagenomics relies on large-scale sequencing of entire microbial communities instead of isolate genomes, leading to new computational challenges. In this article, we outline the major algorithmic approaches for genome assembly and describe recent developments in this domain.
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              Beware of mis-assembled genomes.

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                Author and article information

                Journal
                Evol Bioinform Online
                Evol. Bioinform. Online
                EVB
                spevb
                Evolutionary Bioinformatics Online
                SAGE Publications (Sage UK: London, England )
                1176-9343
                08 May 2018
                2018
                : 14
                : 1176934318774546
                Affiliations
                [1 ]Florida Museum of Natural History and University of Florida, Gainesville, FL, USA
                [2 ]Illinois Natural History Survey, University of Illinois Urbana-Champaign, Champaign, IL, USA
                Author notes
                [*]Julie M Allen, Florida Museum of Natural History and University of Florida, Gainesville, FL 32601, USA. Email: juliema@ 123456ufl.edu
                Article
                10.1177_1176934318774546 EVB-0044190
                10.1177/1176934318774546
                5987885
                29881251
                922c1d35-bf24-49f9-8906-5b47e267088c
                © The Author(s) 2018

                This article is distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 License ( http://www.creativecommons.org/licenses/by-nc/4.0/) which permits non-commercial use, reproduction and distribution of the work without further permission provided the original work is attributed as specified on the SAGE and Open Access pages ( https://us.sagepub.com/en-us/nam/open-access-at-sage).

                History
                : 3 January 2018
                : 9 April 2018
                Categories
                Software or Database Review
                Custom metadata
                January-December 2018

                Bioinformatics & Computational biology
                locus assembly,short-read sequencing,massively parallel sequencing,atram,software

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