Agalma: an automated phylogenomics workflow

Abstract

BackgroundIn the past decade, transcriptome data have become an important component of many phylogenetic studies. They are a cost-effective source of protein-coding gene sequences, and have helped projects grow from a few genes to hundreds or thousands of genes. Phylogenetic studies now regularly include genes from newly sequenced transcriptomes, as well as publicly available transcriptomes and genomes. Implementing such a phylogenomic study, however, is computationally intensive, requires the coordinated use of many complex software tools, and includes multiple steps for which no published tools exist. Phylogenomic studies have therefore been manual or semiautomated. In addition to taking considerable user time, this makes phylogenomic analyses difficult to reproduce, compare, and extend. In addition, methodological improvements made in the context of one study often cannot be easily applied and evaluated in the context of other studies.ResultsWe present Agalma, an automated tool that constructs matrices for phylogenomic analyses. The user provides raw Illumina transcriptome data, and Agalma produces annotated assemblies, aligned gene sequence matrices, a preliminary phylogeny, and detailed diagnostics that allow the investigator to make extensive assessments of intermediate analysis steps and the final results. Sequences from other sources, such as externally assembled genomes and transcriptomes, can also be incorporated in the analyses. Agalma is built on the BioLite bioinformatics framework, which tracks provenance, profiles processor and memory use, records diagnostics, manages metadata, installs dependencies, logs version numbers and calls to external programs, and enables rich HTML reports for all stages of the analysis. Agalma includes a small test data set and a built-in test analysis of these data. In addition to describing Agalma, we here present a sample analysis of a larger seven-taxon data set. Agalma is available for download at https://bitbucket.org/caseywdunn/agalma.ConclusionsAgalma allows complex phylogenomic analyses to be implemented and described unambiguously as a series of high-level commands. This will enable phylogenomic studies to be readily reproduced, modified, and extended. Agalma also facilitates methods development by providing a complete modular workflow, bundled with test data, that will allow further optimization of each step in the context of a full phylogenomic analysis.

Phylogenomic analyses of deep gastropod relationships reject Orthogastropoda

“…All Illumina reads (new and publicly available) were assembled with AGALMA (v. 0.3.4 -0.3.5) [29], 454 datasets were assembled externally with NEWBLER (v. 2.3 and 2.5p1) and gene predictions from Lottia gigantea [30] and Pinctada fucata [31] were imported directly into AGALMA. Source code for most analysis steps as well as sequence alignments, tree sets, summary trees and voucher information are available in a git repository at https:// bitbucket.org/caseywdunn/gastropoda.…”

Re-evaluating the phylogeny of allopolyploid Gossypium L.

“…Many early efforts 76 involving multiple molecular markers (e.g., cpDNA restriction site 77 analysis, rDNA ITS sequencing, nuclear and chloroplast genes) 78 obtained weak or limited resolution (Cronn et al, 1996;DeJoode 79 and Wendel, 1992;Endrizzi et al, 1985;Reinisch et al, 1994;80 Seelanan et al, 1997;Small et al, 1998;Wendel, 1989;Wendel 81 and Albert, 1992;Wendel et al, 1995a,b (Avise and Wollenberg, 1997;Boussau et al, 94 2013; Degnan and Rosenberg, 2009;Eaton and Ree, 2013;95 Mirarab et al, 2014a;Pamilo and Nei, 1988;Rokas et al, 2003;96 Szöll} osi and Daubin, 2012;Szöll} osi et al, 2015). A common 97 approach to overcome this challenge is to use multiple individual 98 loci (Barrett et al, 1991;de Queiroz and Gatesy, 2007;Degnan 99 and Rosenberg, 2006Rosenberg, , 2009Huelsenbeck et al, 1996;Kubatko 100 and Degnan, 2007;Mirarab et al, 2014a;Song et al, 2012;101 Wielstra et al, 2014), and, with the advent of high-throughput 102 genomic technologies, even full phylogenomic data sets consisting 103 of hundreds to thousands of markers distributed throughout the 104 genome (Arbizu et al, 2014;Bond et al, 2014;Boussau et al, 105 2013;Brewer and Bond, 2013;Dunn et al, 2013;Eaton and Ree, 106 2013; Johnson et al,...…”

PIWI proteins and PIWI-interacting RNAs function in Hydra somatic stem cells

“…The transcriptome was assembled using a previously described pipeline (43). piRNA and lineage-specific small RNA mapping was done using Bowtie 0.1.0 (44).…”