ANGSD:analysis of next generation sequencing data

BACKGROUND: High-throughput DNA sequencing technologies are generating vast amounts of data. Fast, flexible and memory efficient implementations are needed in order to facilitate analyses of thousands of samples simultaneously. RESULTS: We present a multithreaded program suite called ANGSD. This program can calculate various summary statistics, and perform association mapping and population genetic analyses utilizing the full information in next generation sequencing data by working directly on the raw sequencing data or by using genotype likelihoods. CONCLUSIONS: The open source c/c++ program ANGSD is available at http://www.popgen.dk/angsd. The program is tested and validated on GNU/Linux systems. The program facilitates multiple input formats including BAM and imputed beagle genotype probability files. The program allow the user to choose between combinations of existing methods and can perform analysis that is not implemented elsewhere. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-014-0356-4) contains supplementary material, which is available to authorized users

Genomic diversity and novel genome-wide association with fruit morphology in <i>Capsicum</i>, from 746k polymorphic sites

Capsicum is one of the major vegetable crops grown worldwide. Current subdivision in clades and species is based on morphological traits and coarse sets of genetic markers. Broad variability of fruits has been driven by breeding programs and has been mainly studied by linkage analysis. We discovered 746k variable sites by sequencing 1.8% of the genome in a collection of 373 accessions belonging to 11 Capsicum species from 51 countries. We describe genomic variation at population-level, confirm major subdivision in clades and species, and show that the known major subdivision of C. annuum separates large and bulky fruits from small ones. In C. annuum, we identify four novel loci associated with phenotypes determining the fruit shape, including a non-synonymous mutation in the gene Longifolia 1-like (CA03g16080). Our collection covers all the economically important species of Capsicum widely used in breeding programs and represent the widest and largest study so far in terms of the number of species and number of genetic variants analyzed. We identified a large set of markers that can be used for population genetic studies and genetic association analyses. Our results provide a comprehensive and precise perspective on genomic variability in Capsicum at population-level and suggest that future fine genetic association studies will yield useful results for breeding

Passagerernes kollektive transport eller den kollektive transports passagerer? Muligheder og faldgruber ved brugerinddragelse i planlægningen af kollektiv transport

Passagererne i den kollektive transport står i en svagere position end forbrugere på andre markeder, idet det sjældent er muligt at vælge en anden udbyder, hvis man er utilfreds. Dette fravær af traditionelle markedsmekanismer kan være en medvirkende årsag til frustrationer og afmagt hos passagererne, der oplever at vigtige beslutninger træffes langt fra deres hverdag.&nbsp; Brugerinddragelse kan være en måde for myndigheder og trafikselskaber til at skabe større overensstemmelse mellem den udbudte kollektive transport og passagerernes ønsker. Resultater tyder da også på, at der er en vis sammenhæng mellem graden af brugerinddragelse og tilfredshed med den kollektive transport.&nbsp; Med udgangspunkt i både teori og praksis vil vi redegøre for de muligheder og faldgruber brugerinddragelse kan give. Anvendes brugerinddrages på denne rette måde, kan det være med til at imødegå frustrationer hos passagererne og give medejerskab for vigtige beslutninger. Omvendt kan uhensigtsmæssig anvendelse af brugerinddragelse, eller fravær af brugerinddragelse blive dyrere for samfundet, når beslutninger må ændres eller gøres om.&nbsp