Assembly of Solexa tomato reads

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

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RESULTS BAC coverage before assembly
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RESULTS BAC recovery after assembly (VELVET
Zerbino Birmey http//www.ebi.ac.uk/zerbino/vel
vet/) 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)
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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