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Assembly of Solexa tomato reads

Assembly of Solexa tomato reads. Mar í a Jos é Truco Bioinformatics and Genomics Program CRG-Centre de Regulació Gen ò mica Barcelona. RESULTS : Testing of the three tomato run concentrations. Methodology: -Mixture of 9 BACs (2 incomplete). Three concentration runs: 1 pM , 2pM and 4 pM

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Assembly of Solexa tomato reads

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  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 • 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 0 0 20000 40000 60000 80000 100000

  4. RESULTS: BAC recovery after assembly (VELVET:Zerbino &Birmey; http://www.ebi.ac.uk/~zerbino/velvet/) using sequences from 4pM run (3920769 sequences) and 1 pM run (1627900 sequences) 4pM run: BAC recovery 66.4-89% (81.3-94.6%) 1pM run: BAC recovery 45.1-82.4% (66-97.6%) 2500 2000 1500 1000 500 0 0 20000 40000 60000 80000 100000

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

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