MaizeGDB is a community-oriented, long-term, federally funded
informatics service to researchers focused on the crop plant and
model organism Zea mays.
MaizeGDB is a founding member of
AgBioData,
a consortuim of agriculture-related online resources which is
committed to making agriculture-related research data FAIR.
GCV: A web-app that visualizes genomic context data in a single, federated interface by using functional annotations as a unit of search and comparison.
De novo genome assembly of tropical maize inbred line CML247
Project PI
Fei Lu, Edward Buckler
Project start date
2014
Release date
5/30/2016
Publication status
published
Project reference
High-resolution genetic mapping of maize pan-genome sequence anchors.
Lu F, Romay MC, Glaubitz JC, Bradbury PJ, Elshire RJ, Wang T, Li Y, Li Y, Semagn K, Zhang X, Hernandez AG, Mikel MA, Soifer I, Barad O, Buckler ES
At MaizeGDB DOI
Sequence service provider: Library Prep by University of Illinois / Sequenced by Cornell University Sequencing technologies: Illumina HiSeq2500, Illumina MiSeq Sequencing method: Illumina HiSeq2500, Illumina MiSeq Genome coverage: 130x
Assembly description
Assembly methods: DenovoMAGIC Construction of pseudomolecules: Scaffolds were ordered and oriented
The length of scaffold which takes the sum length (summing from longest to shortest scaffold) past 50% of the total assembly size.
How many scaffolds are counted in reaching the N50 threshold.
The length of scaffold which takes the sum length (summing from longest to shortest scaffold) past 90% of the total assembly size.
How many scaffolds are counted in reaching the N90 threshold.
A contig is a contiguous consensus sequence that is
derived from a collection of overlapping reads.
A scaffold is set of a ordered and orientated contigs
that are linked to one another by mate pairs of sequencing reads.
