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View Coffee Transcriptome New Assembly As of January 2012

1. Re- assembly of ESTs

Vector and bacterial contaminant removal

Pipeline: Seqclean

Result: analyzed 200,347 seqs
Trimmed = 13
Trashed = 251 (vector and bacterial contaminants)
Short = 247

Re-assembly:
Contigs = 19,822
Singletons = 19,036

2. Hybrid Assembly with CLC

Assembly of ESTs + Illumina

Input:
Illumina Trinity assembly + CAP3 Sanger assembly

Assembler: CLC

RESULT: CarabicaBGItrim_CenicafeCArabica.fasta = 55554 Contigs: Hybrid Assembly CENICAFE ESTs + RNASeq BGI China – Assembly with CLC.

Average size = 826bp

3. Hybrid Assembly with CAP3

RNAseq Trinity Assembly (41,140 seqs) + Cenicafe49 ESTs (40,038)
Assembly file: /data/process/Cafe/Transcriptomics/ESTsRNAseqAssembly/ESTsRNAseqCAP3Assembly.fasta
Sequences= 52,539 contigs (14,246) + singletons (38293)

RNAseqUnigenes average size = 561bp
Carabica 49 ESTs average size = 819bp
RNAseq + ESTs CAP3 hybrid assembly = 764bp

3. Unigene of Illumina Contigs using Proteins as Linkers

41,143 unigenes

BLASTn (1e-20) vs C.arabica Cenicafe ESTs (Database)= 23540 hits (57,2%)
BLASTn (1e-20) vs C.arabica Cenicafe ESTs (Query)= 27964 hits (69,9%)