Download Easy de novo assembly reference

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 Easy de novo assembly reference
Sequence Length
104
Coverage
0.0
Error rate
0/1000 bases
Polymorphisms
Sequence contains 0 polymorphisms
Gigsaw created by Dr David Martin, University of Dundee, Scotland
Easy de novo assembly reference sheet 0 forward reference sequence
104
X A T A
90
100
X A A T T T C G A T G C T A G C T A G C T
70
80
X G C G A T A C A G C A T G C T C G G C T
50
60
X A T C G A T C G A T C G A C G C G C A T
30
40
X A T C G A G C G G C G G A T T A T T A T
1
10
20
A C T G A C T G G T T G C A A T A C G G C
Gigsaw created by Dr David Martin, University of Dundee, Scotland
Easy de novo assembly reference sheet 0 reverse reference sequence
1
T A T A
10
20
X G C T A G C T A G C A T C G A A A T T A
30
40
X G C C G A G C A T G C T G T A T C G C A
50
60
X T G C G C G T C G A T C G A T C G A T A
70
80
X T A A T A A T C C G C C G C T C G A T G
90
100
104
X C C G T A T T G C A A C C A G T C A G T
Gigsaw created by Dr David Martin, University of Dundee, Scotland