NGSEP3: accurate variant calling across species and sequencing protocols

Tello, Daniel; Gil, Juanita; Loaiza, Cristian D; Riascos, John J.; Cardozo, Nicolás; Duitama, Jorge

doi:10.1093/bioinformatics/btz275

Cited by 63 publications

(72 citation statements)

References 49 publications

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“…SNP calling was carried out as described by Gil et al (2019). Briefly, the GBS reads were demultiplexed using NGSEP (v3.3.0) (Tello et al, 2019). Adapters and low quality bases from the raw sequencing data were trimmed using Trimmomatic (v0.36) (Bolger et al, 2014), and the processed reads were aligned to the reference genome of P. vulgaris G19833 v2.1.…”

Section: Snp Calling and Population Structurementioning

confidence: 99%

Genomic Prediction of Agronomic Traits in Common Bean (Phaseolus vulgaris L.) Under Environmental Stress

et al. 2020

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Section: Snp Calling and Population Structurementioning

confidence: 99%

Genomic Prediction of Agronomic Traits in Common Bean (Phaseolus vulgaris L.) Under Environmental Stress

et al. 2020

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“…Bioinformatic analysis of diversity GBS data. The sequences obtained from each sample were de-multiplexed by their barcode using Next Generation Sequencing Experience Platform (NGSEP) V3.3.2 85 . Individual fastq files were mapped to the Lima bean reference genome by using default parameters of bowtie2 and adding an ID code for each accession 84 .…”

Section: Genetic Diversity and Population Structure Analysesmentioning

confidence: 99%

Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean

García

Duitama

Zullo

et al. 2020

Preprint

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Lima bean (Phaseolus lunatus L.) is one of the five domesticated Phaseolus bean crops, which are essential sources of dietary proteins for human consumption. Compared to common bean (P. vulgaris), it shows a wider range of ecological adaptations along its distribution range from Mexico to Argentina. These adaptations and its phenotypic plasticity make Lima bean a promising crop for improving food security under predicted scenarios of climate change in Latin America and elsewhere. Lima bean is also an excellent model to study convergent evolution of the adaptive domestication syndrome due to its dual domestication in Mesoamerica and the Andes. Combining long and short read sequencing technologies with a dense genetic map from a biparental population, we obtained the first chromosome-level genome assembly for Lima bean. Annotation of 28,326 gene models showed high diversity among 1,917 genes with conserved domains related to disease resistance. Structural comparison across 21,180 orthologs with common bean revealed high genome synteny and two large intrachromosomal rearrangements. Speciation between P. lunatus and P. vulgaris occurred about six million years ago according to nucleotide evolution between these orthologs. Population genomic analysis of GBS data for 482 wild and domesticated accessions from the Mesoamerican and Andean gene pools provided novel evidence on population structure at a finer geographical scale. Results show that wild Lima bean is organized into six clusters with mostly non-overlapping distributions and that Mesomerican landraces can be further subdivided into three subclusters. A new wild cluster of diversity was found in the Colombian Andes and a separate genetic cluster was observed for Mesoamerican landraces of the Peninsula of Yucatan in Mexico. This study also documents genome wide patterns of selection and haplotype introgression events among gene pools. Analysis of RNA-seq data obtained from wild and domesticated accessions at two different pod developmental stages revealed 4,275 differentially expressed genes, which could be related to pod dehiscence and seed development. We expect that the present resources serve as a solid basis to achieve a comprehensive view of the degree of convergent evolution of Phaseolus species under domestication and provide new tools and information for breeding for climate change resiliency of different domesticated species.

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“…3.a), a GWASpoly format ( [Rosyara et al, 2016]) ( Fig. 3.b), and Variant Call Format (VCF) (Fig.3.c) which is transformed into GWASpoly format using NGSEP 4.0.2 ( [Tello et al, 2019]). The phenotype file contains only one trait with the first column for the sample names and the second column for the trait values ( Fig.…”

Section: Reading Configuration Filementioning

confidence: 99%

“…The following lines contain genotype information of the samples for each position. VCF marker data can be encoded as simple genotype calls (GT format field, e.g., 0/0/1/1 for tetraploids or 0/1 for diploids) or using the NGSEP custom format fields ( [Tello et al, 2019]): ACN, ADP or BSDP. d. Phenotype file in a matrix format with column headers and sample names followed by their trait values.…”

Section: Amentioning

confidence: 99%

MultiGWAS: An integrative tool for Genome Wide Association Studies (GWAS) in tetraploid organisms

Garreta

Cerón‐Souza

Palacio

et al. 2020

Preprint

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The Genome-Wide Association Studies (GWAS) are essential to determine the genetic bases of either ecological or economic phenotypic variation across individuals within populations of model and non-model organisms. For this research question, current practice is the replication of the GWAS testing different parameters and models to validate the reproducibility of results. However, straightforward methodologies that manage both replication and tetraploid data are still missing. To solve this problem, we designed the MultiGWAS, a tool that does GWAS for diploid and tetraploid organisms by executing in parallel four software, two for polyploid data (GWASpoly and SHEsis) and two for diploids data (PLINK and TASSEL). MultiGWAS has several advantages. It runs either in the command line or in an interface. It manages different genotype formats, including VCF. It executes both the full and naive models using several quality filters. Besides, it calculates a score to choose the best gene action model across GWASPoly and TASSEL. Finally, it generates several reports that facilitate the identification of false associations from both the significant and the best-ranked association SNP among the four software. We tested MultiGWAS with tetraploid potato data. The execution demonstrated that the Venn diagram and the other companion reports (i.e., Manhattan and QQ plots, heatmaps for associated SNP profiles, and chord diagrams to trace associated SNP by chromosomes) were useful to identify associated SNP shared among different models and parameters. Therefore, we confirmed that MultiGWAS is a suitable wrapping tool that successfully handles GWAS replication in both diploid and tetraploid organisms.

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NGSEP3: accurate variant calling across species and sequencing protocols

Cited by 63 publications

References 49 publications

Genomic Prediction of Agronomic Traits in Common Bean (Phaseolus vulgaris L.) Under Environmental Stress

Genomic Prediction of Agronomic Traits in Common Bean (Phaseolus vulgaris L.) Under Environmental Stress

Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean

MultiGWAS: An integrative tool for Genome Wide Association Studies (GWAS) in tetraploid organisms

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