Sequence Files

Illumina – 454 Files
Coffee Rust NGS Data Registry

Assembly Project:

Preliminary Analysis of Raw Data Sequences: Illumina.
Preliminary Analysis of Raw Data Sequences: 454.

454 Genome Assembly using CLC
Illumina Genome Assembly using CLC
Hybrid Assembly of 454 and Illumina data with CLC
Second Hybrid Assembly of 454 and Illumina data with CLC
Third Hybrid Assembly of 454 and Illumina data with CLC
Rust Illumina Assembly of Differents Strains
Mira and CLC Assembly 454 Reads- HvCat Illumina

Genome Assembly using CLC: Test and Paired Size Insert Measurement
Genome Assembly using SOAPdenovo: Test

Hemileia v. vs Hypotenemus h comparison
Genome Assembly Comparison
MIRA Vs Newbler: old assembly with 1/2 plate of 454

QC

Megan
Fastq screen

Rust Annotation of Individual Assemblies

Rust Illumina Assembly of Differents Strains
ITS Analysis
Roya Blast Homology
Roya Blast other sequences
Mitochondrion Rust
Gene Prediction
Protein families Annotation
Secretome Annotation
Comparison Between Common and Unique Sequences in All Astrains
Running Cegma to All Assemblies
Masking CLC Assemblies
File:Resultados Preliminares David Botero.docx

Rust Annotation of Third Hybrid Assembly

SSRs Roya Third Hybrid Assembly
TEs Roya Third Hybrid Assembly

Rust Transcriptomes

Data Cleansing and Preparation
Assemblies with Trinity
Mapping of Transcriptome to Genome
BLAST Sequence Analysis
Blast Homolgy to H.vastatrix published sequences
Discovering novel genes and transcripts – Identifying differentially expressed and regulated genes
Discovering novel genes and transcripts – CLCAssemblyAll454HvCatIllum
Comparison Between Common and Unique Sequences in All Transcriptomes
Megan Transcriptome

Patogenicity

WoLF PSORT
NucPred
SignalP 4.0
PProwler

Databases

Rust Database

Analysis and Information of 2010:

Related Genome Projects
Genome Size-Chromosome Number
Fungi Database Repositories
Gene Prediction
Maker results
GBrowse
Chado
SNPs Single Nucleotide Polimorfism Prediction on Coffee Rust Genome
Pathways
Secretome Proteins
B2G Roya
TEs Roya
SSRs Roya
Phenotypic Characterization
Blast Homology Results
Ecp6 Proteins

David Notes