Comparing Sequencers read length bases per machine run 10 bp1,000 bp200 bp 1 Gb 100 Mb 1Mb 100Gb Illumina, AB/SOLiD short-read sequencers ABI capillary sequencer 454 pyrosequencer (20-100 Mb in 300-400 bp reads) (100Gb in 25-50 bp reads)
… and they give you the picture on the box Read mapping Read mapping is like doing a jigsaw puzzle… …you get the pieces… Problem is, some pieces are easier to place than others…
Alignment of reads Reads generated from sequencing is mapped to a reference genome Conventional tools like Blast or Blat do not work well with short sequence reads. Modification of existing alignment algorithms to handle short reads.
Inversion detected by paired-end data Total Inversions Span exon(s) or gene(s) IntronsIntergenic 2915078163
Copy Number Variations (CNVs) Total CNVsGainsLosses 21,7397,18214,557 Graubert, et al. 2007 PLoS Genetics Anderson, et al. 2005 Genes & Immunity Several gene members of Klra family was deleted in DBA/2J
De novo assembly ABySS ALLPATHS Euler-SR SHRAP SSAKE Velvet SOAP