DOI: 10.5061/dryad.qn1n2
title: Data from: Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies

description: As a greater number and diversity of high-quality vertebrate reference
 genomes become available, it is increasingly feasible to use these
 references to guide new draft assemblies for related species.
 Reference-guided assembly approaches may substantially increase the
 contiguity and completeness of a new genome using only low levels of
 genome coverage that might otherwise be insufficient for de novo genome
 assembly. We used low-coverage (~3.5–5.5x) Illumina paired-end sequencing
 to assemble draft genomes of two bird species (the Gunnison Sage-Grouse,
 Centrocercus minimus, and the Clark's Nutcracker, Nucifraga
 columbiana). We used these data to estimate de novo genome assemblies and
 reference-guided assemblies, and compared the information content and
 completeness of these assemblies by comparing CEGMA gene set
 representation, repeat element content, simple sequence repeat content,
 and GC isochore structure among assemblies. Our results demonstrate that
 even lower-coverage genome sequencing projects are capable of producing
 informative and useful genomic resources, particularly through the use of
 reference-guided assemblies.
description: Sage-Grouse de novo
 assemblyDe novo assembly of the
 Gunnison Sage-Grouse using CLC Genomics Workbench. Includes CLC assembly
 report.Sage_Grouse_denovo_assembly_07-17-2013_DCC.tar.bz2Clark's Nutcracker de novo assemblyDe novo assembly of the Clark's Nutcracker using CLC Genomics Workbench. Includes CLC assembly report.Clarks_Nutcracker_denovo_assembly_07-17-2013_DCC.tar.bz2Sage-Grouse to Chicken chromosome annotationChromsome annotation of the Sage-Grouse using the Chicken genome. Used 1x reference-guided assembly and blast, and assumed high synteny between species.SG_chrs.tar.bz2Clark's Nutcracker to Zebra Finch chromosome annotationChromosome annotation of the Clark's Nutcracker using the Zebra Finch genome. Used 1x reference-guided assembly and blast, and assumed high synteny between species.CN_chrs.tar.bz2Sage-Grouse 1x reference-guided genome1x consensus Sage-Grouse genome from reference-guided assembly using the Chicken genome as reference. Assembly statistics report is included.SG_1x_guided_consensus.tar.bz2Sage-Grouse 2x reference-guided genome2x consensus Sage-Grouse genome from reference-guided assembly using the Chicken genome as reference. Assembly statistics report is included.SG_2x_guided_consensus.tar.bz2Sage-Grouse 5x reference-guided genome5x consensus Sage-Grouse genome from reference-guided assembly using the Chicken genome as reference. Assembly statistics report is included.SG_5x_guided_consensus.tar.bz2Sage-Grouse mitochondrial assembly and MITOS annotationReference-guided assembly of the Sage-Grouse mitochondrion using consensus Galliformes mitochondrial sequence as guide. Includes MITOS annotation.SG_MITOS_MtGenomes_Annotation.tar.bz2Clark's Nutcracker 1x reference-guided genome1x consensus Clark's Nutcracker genome from reference-guided assembly using the Zebra Finch genome as reference. Assembly statistics report is included.CN_1x_guided_consensus.tar.bz2Clark's Nutcracker 2x reference-guided genome2x consensus Clark's Nutcracker genome from reference-guided assembly using the Zebra Finch genome as reference. Assembly statistics report is included.CN_2x_guided_consensus.tar.bz2Clark's Nutcracker 5x reference-guided genome5x consensus Clark's Nutcracker genome from reference-guided assembly using the Zebra Finch genome as reference. Assembly statistics report is included.CN_5x_guided_consensus.tar.bz2Clark's Nutcracker mitochondrial assembly and MITOS annotationReference-guided assembly of the Clark's Nutcracker mitochondrion using consensus Corvidae mitochondrial sequence as guide. Includes MITOS annotation.CN_MITOS_MtGenomes_Annotation.tar.bz2