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As part of the CRDF grant mandate, we provide services related to sequence assembly and analysis to the Citrus Greening-HLB community. We are presently assisting several groups with the goal of reducing the time between generation of raw data and its workup into a state appropriate for public release. Some of the expertise that CG-HLB personnel can provide are listed below. Contact us for more information.
| service |
description |
you provide |
we return |
| de novo assembly of reads from Sanger and Next generation sequencing technologies |
Collaborations are invited for assembly and scaffolding of reads from Illumina, 454 and Sanger sequencing technologies. We have access to a 64GB RAM server and expertise in various tools such as Velvet, MIRA3, Phred etc. for de novo and mapping assembly. We use scaffolders like SSPACE, SOPRA and Minimus2 for post-assembly clustering. Once assembled, we will work closely with you towards your ultimate goal, whether that is closing the genome or designing diagnostic markers in unique regions. |
DNA sequence reads |
Contigs and/or scaffolds |
| Annotation |
We will work with you in a iterative process to annotate and analyze draft genomes and scaffolds using RAST, Mauve and NCBI databases. |
Draft genomes, contigs or scaffolds |
Whole genome annotation including genes and repeats |
| Data hosting |
We can host sequence datasets in any commonly used format (Fasta, Genbank, etc.) on our website. We can incorporate your data into our community genome browser, if desired. We can also provide customized solutions where your data/genome browser is password-protected and accessible to only your research community. |
Sequence datasets or annotations |
Online access that can be publicly accessible or user-restricted |
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