1. Assembly of Solexa tomato reads
María José Truco
Bioinformatics and Genomics Program
CRG-Centre de Regulació Genòmica
Barcelona

2. RESULTS: Testing of the three tomato run concentrations
Methodology:
-Mixture of 9 BACs (2 incomplete). Three concentration runs: 1 pM, 2pM and 4 pM
-Alignment to Reference Genomes using ELAND (Solexa)
Sequences are aligned if have no more than 2 mismatches exists and align only to a single location of the reference genome
~ 30% of the sequences are contamination from E. coli and vector
1pM
2pM
4pM
Sequences %
sequences
E. coli
632242
25.8
25.5
23.4
pBeloBAC11
96316
3.9
170772
4.0
220972
Yeast
84480
3.5
151431
194927
3.4
Human BACs* 84
0.0 68 75
Tomato BACs
41.0
43.1
46.8
Repeats**
414523
16.9
702356
16.3
854140
15.0
Non-matching***
218044
8.9
336869
7.8
418374
7.4
All reads
Testing for contamination during sample preparation
** Reads matching 2 or more sites in the reference genomes
** * Reads with more than 2 mismatches or not aligning to any reference genome

3. RESULTS: BAC coverage before assembly
500
400
300
200
100

4. RESULTS: BAC recovery after assembly (VELVET: Zerbino &Birmey; using sequences from 4pM run ( sequences) and 1 pM run ( sequences)
4pM run: BAC recovery % ( %)
1pM run: BAC recovery % ( %)
2500
2000
1500
1000
500

5. RESULTS: Gap filling of incomplete BAC EF606852
Methodology:
-Selection of two fragments of ~4Kb flanking the gap
-Blast assembled contigs against the two sequences flanking the gap
4121 25
left gap flanking region
4153
7297
right gap flanking region
GAP 25
4121
4153
7297
12372
perfect match
mis
match
assembled contig
left gap flanking region
right gap flanking region