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Roche 454 reads of genotype 1 Contamination check BLASTN against chloroplast and mitochondrial sequences Remove contaminations Artificial replicate check Cluster reads to remove duplicates Repeat read classification Repeat annotation report Unique repeat junction (RJ) annotation (RJPrimers) Single-copy RJ sequences or reads Assembly Single-copy gene-related contigs and singletons Remove artificial duplicates Repeat annotation BLASTN against known repeat databases Characterized repeat reads and annotation Remove repeat reads Gene annotation BLAST against gene databases (genes, unigenes, proteins) Characterized Gene-related reads and annotation (gsAssembler) Remove characterized gene reads Mapping to cDNA SOliD or Solexa reads in another genotype (AS75) Uncharacterized gene-related reads Remove uncharacterized gene reads Uncharacterized read annotation Mapping to genomic SOliD or Solexa reads in another individual (AS75) Read mapping depth > a cutoff Single-copy uncharacterized sequences Uncharacterized repeat sequences
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