RT Journal Article SR Electronic T1 FGMP: assessing fungal genome completeness and gene content JF bioRxiv FD Cold Spring Harbor Laboratory SP 049619 DO 10.1101/049619 A1 Ousmane H. Cissé A1 Jason E. Stajich YR 2016 UL http://biorxiv.org/content/early/2016/04/20/049619.abstract AB Motivation: Inexpensive high-throughput DNA sequencing has democratizing access to genetic information for most organisms so that access to a genome or transcriptome of an organism is not limited to model systems. However, the quality of the sampled genomes can vary greatly which hampers utility for comparisons and meaningful interpretation. The uncertainty of the completeness of a given genome sequence can limit feasibility of asserting patterns of high rates of gene loss reported in many lineages.Results We propose a computational framework and sequence resource for assessing completeness of fungal genomes called FGMP (Fungal G enome M apping Project). Our approach is based on evolutionary conserved sets of proteins and ultra conserved DNA elements and is applicable to various types of genomic data. We present a comparison of FGMP with state-of-the-art methods utilizing 246 genome assemblies of fungi. We discuss genome assembly improvements/degradations in 56 two-point fungal genome assemblies, as recorded by NCBI assembly archive.Availability and Implementation FGMP software and datasets are freely available from https://github.com/stajichlab/FGMP or biocluster.ucr.edu/~ocisse/manuscript/FGMP.v.1.0.tar.gzContact ousmanecis{at}gmail.com or jason.stajich{at}ucr.eduSupplementary information Supplementary data are available at biocluster.ucr.edu/~ocisse/manuscript.