Read depth 1 2 3. 4. 3 2 1 gap width reference. SNP. Variant possible sequence error. Gigsaw created by Dr David Martin, University of Dundee, Scotland ...
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. &ŽƌƉĂŝƌĞĚĞŶĚƌĞĂĚƐ͕ĐĂƌĞĨƵůůLJĚŝǀŝĚĞƚŚĞŵĂƐƐŚŽǁŶŝŶƚŚĞĮŐƵƌĞďĞůŽǁ
The reference sequence can be assembled by using the grey box on the row end as a tab on which ƚŽƐƟĐŬƚŚĞƉƌĞǀŝŽƵƐƐĞƋƵĞŶĐĞƉŽƌƟŽŶ;ƉŽƐŝƟŽŶƐĂƌĞŶƵŵďĞƌĞĚĂďŽǀĞƚŚĞƐĞƋƵĞŶĐĞͿ͘
For a normal assembly, try to overlap the reads as much as possible. You should end up with approximately ƚŚĞƌĞĂĚĚĞƉƚŚŽĨƌĞĂĚƐĂƚĂůůƉŽŝŶƚƐŝŶƚŚĞĮŶĂůĂƐƐĞŵďůLJ͘ZĞŵĞŵďĞƌƚŚĂƚƚŚĞƌĞǀĞƌƐĞĐŽŵƉůĞŵĞŶƚƐĞƋƵĞŶĐĞ ;ƚŚĞŽƚŚĞƌƐƚƌĂŶĚŽĨEͿĐĂŶďĞĨŽƵŶĚŽŶƚŚĞƌĞǀĞƌƐĞƐŝĚĞ͘
Read depth 1 2 3 4 3 2 1 &ŽƌƉĂŝƌĞĚĞŶĚƌĞĂĚƐ͕ƉůĂĐĞƚŚĞŵĨĂĐŝŶŐĞĂĐŚŽƚŚĞƌĂƉƉƌŽdžŝŵĂƚĞůLJƚŚĞŐĂƉƐŝnjĞĂƉĂƌƚ͘ŐĂŝŶĂƩĞŵƉƚƚŽĂůŝŐŶ them as well as you can.
gap width
&ŽƌĂůŝŐŶŝŶŐĂŐĂŝŶƐƚƚŚĞƌĞĨĞƌĞŶĐĞƐĞƋƵĞŶĐĞ͕ƚƌLJƚŽĮŶĚƚŚĞƉŽƐŝƟŽŶǁŚĞƌĞƚŚĞƐĞƋƵĞŶĐĞďĞƐƚŵĂƚĐŚĞƐ͘/ĨLJŽƵĂƌĞ 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 Ben PLUS Sequence Length
92
Coverage
4.6
Error rate
10/1000 bases
Polymorphisms
Sequence contains 0 polymorphisms
Gigsaw created by Dr David Martin, University of Dundee, Scotland
Ben PLUS sheet 1 forward reads
G G G C A A G G T G A A C G T G G A T G A C C C C A C A G G G C A G T A A C G G C A G G T G A A C G T G G A T G A A G T T G G A C C A A C T T C A T C C A C G T T C A C G T T G G T G G T G A G G C C C T G G G C C T G A C T C C T G A G G A G A A G T C T A G A C T T C T C C T C A G G A G T C A G G G G C A A G G T G A A C G T G G A T G A C C T T G C C C C A C A G G G C A G T A A T C A C C A C C A A C T T C A T C C A C G C A A G G T G A A C G T G G A T G A A G T T G A G G A G A T G T C T G C C G T T A C G T G A A C G T G G A T G A A G T T G G T A C A A G G C A G T A A C G G C A G A C T C T G G T G C A T C T G A C T C C T G A G X A A T C T G A C T C C T G A G G A G A A G T C C A C A G G G C A G T A A C G G C A G A G C A G T A A C G G C A G A C T T C T C C C C A C G T T C A C C T T G C C C C A C A C T G A G G A G A A G T C T G C C G T T A Gigsaw created by Dr David Martin, University of Dundee, Scotland
Ben PLUS sheet 1 reverse reads
T C A T C C A C G T T C A C C T T G C C C T G C C G T T A C T G C C C T G T G G G G C C A A C T T C A T C C A C G T T C A C C G T G A A C G T G G A T G A A G T T G G T G C C C A G G G C C T C A C C A C C A A C A G A C T T C T C C T C A G G A G T C A G C T G A C T C C T G A G G A G A A G T C T T C A T C C A C G T T C A C C T T G C C C T T A C T G C C C T G T G G G G C A A G G C G T G G A T G A A G T T G G T G G T G A A C T T C A T C C A C G T T C A C C T T G G T A A C G G C A G A C A T C T C C T C A A C C A A C T T C A T C C A C G T T C A C A G T C T G C C G T T A C T G C C T T G T C T C A G G A G T C A G A T G C A C C A G A C T T C T C C T C A G G A G T C A G A T T C T G C C G T T A C T G C C C T G T G G G G A G A A G T C T G C C G T T A C T G C T G T G G G G C A A G G T G A A C G T G G T A A C G G C A G A C T T C T C C T C A G Gigsaw created by Dr David Martin, University of Dundee, Scotland
Gigsaw Next Gen Sequence Assembly Simulator ... Make sure that reads sheet 1 forward is on the back of the same sheet of paper as reads sheet 1 reverse and.
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