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lecture-8 - Practical Bioinformatics for Life Scientists...

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Practical Bioinformatics for Life Scientists Week 4, Lecture 8 István Albert Bioinformatics Consulting Center Penn State
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Reminder Before any serious work re-check the documentation for small but essential details. Example: bwa needs to be indexed differently for small and large genomes bwa has to be invoked with different alignment modes for short reads (200 < ) and long reads (200 >)
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Sequencing Coverage (Depth) Lander/Waterman model: 1. random reads 2. ability to detect overlap does not change coverage C = N * L / G N = number of reads, L = length of reads, G = size of genome Probability of a base not being sequenced P = exp(-C) To get the percent of genome not covered (multiply by 100) N=35 million, L=35, G=250 million C = 5 0.6% genome not sequenced 15 million bases not covered
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Realistic coverage Neither of the models assumptions are correct multiply required coverage at least 10 fold What part of the genome is coverable to begin with?
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