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Gigsaw Next Gen Sequence Assembly Simulator Print out the sequence reads and reference sequence sheets. Make sure that reads sheet 1 forward is on the back of the same sheet of paper as reads sheet 1 reverse and ensure that the reads align. Cut out the reads along the white horizontal gaps. For paired end reads, carefully divide them as shown in the figure below The reference sequence can be assembled by using the grey box on the row end as a tab on which to stick the previous sequence portion (positions are numbered above the sequence). For a normal assembly, try to overlap the reads as much as possible. You should end up with approximately the read depth of reads at all points in the final assembly. Remember that the reverse complement sequence (the other strand of DNA) can be found on the reverse side. Read depth 1 2 3 4 3 2 1 For paired end reads, place them facing each other approximately the gap size apart. Again attempt to align them as well as you can. gap width For aligning against the reference sequence, try to find the position where the sequence best matches. If you are looking for SNPs or have a high error rate then there may not be a perfect match. SNP Variant possible sequence error reference Gigsaw created by Dr David Martin, University of Dundee, Scotland Gigsaw Parameters for Mutation reference Sequence Length 117 Coverage 0.0 Error rate 15/1000 bases Polymorphisms Sequence contains 0 polymorphisms Gigsaw created by Dr David Martin, University of Dundee, Scotland Mutation reference sheet 0 forward reference sequence 110 117 X G C C C A C C A T C G A C G A G 90 100 X G A G G C C A G C G A G G A C C C C G A 70 80 X T G G A G A G C G C C G A C A T C A G C 50 60 X C G G C G A G A A C G A G G G C A T C G 30 40 X A A C A G C C T G G C C A C C G A G G A 1 10 20 G C C G C C A T G T A C A C C A G G G C C Gigsaw created by Dr David Martin, University of Dundee, Scotland Mutation reference sheet 0 reverse reference sequence 1 10 C T C G T C G A T G G T G G G C T 20 30 X C G G G G T C C T C G C T G G C C T C G 40 50 X C T G A T G T C G G C G C T C T C C A C 60 70 X G A T G C C C T C G T T C T C G C C G T 80 90 X C C T C G G T G G C C A G G C T G T T G 100 110 117 X G C C C T G G T G T A C A T G G C G G C Gigsaw created by Dr David Martin, University of Dundee, Scotland